SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_020563176.1 NCBI__GCF_000372865.1:WP_020563176.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

1dfoB Crystal structure at 2.4 angstrom resolution of e. Coli serine hydroxymethyltransferase in complex with glycine and 5-formyl tetrahydrofolate (see paper)
69% identity, 100% coverage: 1:416/418 of query aligns to 1:416/417 of 1dfoB

query
sites
1dfoB

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active site: Y55 (= Y55), E57 (= E57), D200 (= D201), T226 (= T227), K229 (= K230), R235 (= R236)
binding N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid: E57 (= E57), Y64 (= Y64), Y65 (= Y65), L121 (= L121), G125 (= G125), H126 (= H126), L127 (= L127), S175 (= S176), S245 (≠ N245), E247 (= E247), N347 (= N347), S355 (= S355), P356 (= P356), F357 (= F357)
binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: S35 (= S35), Y55 (= Y55), Y65 (= Y65), S97 (= S97), G98 (= G98), S99 (= S99), H126 (= H126), F174 (= F175), S175 (= S176), D200 (= D201), A202 (= A203), H203 (= H204), K229 (= K230), G262 (= G262), R363 (= R363)

P0A825 Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 from Escherichia coli (strain K12) (see 8 papers)
69% identity, 100% coverage: 1:416/418 of query aligns to 1:416/417 of P0A825

query
sites
P0A825

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K54 (= K54) modified: N6-acetyllysine
Y55 (= Y55) mutation to F: 50 and 15-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 4-fold decrease in the catalytic efficiency.
K62 (= K62) modified: N6-succinyllysine
Y65 (= Y65) mutation to F: Decrease in catalytic activity.
L85 (= L85) mutation to A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-276.
P214 (= P215) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type.; mutation to G: No significant difference in catalytic efficiency and affinity compared to the wild-type.
P216 (= P217) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type. Alteration in the folding rate.; mutation to G: Important decrease in affinity and catalytic efficiency. Severely compromised in folding into a catalytically competent enzyme.
P218 (= P219) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type.; mutation to G: No significant difference in catalytic efficiency and affinity compared to the wild-type.
H228 (= H229) Plays an important role in substrate specificity; binding pyridoxal 5'-phosphate; mutation H->D,N: Utilize substrates and substrate analogs more effectively for a variety of alternate non-physiological reactions.
K229 (= K230) modified: N6-(pyridoxal phosphate)lysine
R235 (= R236) binding pyridoxal 5'-phosphate; mutation to K: 1500- and 20-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 15-fold decrease in the catalytic efficiency.; mutation to L: 450- and 11-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 60-fold decrease in the catalytic efficiency.; mutation to Q: 900- and 17-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 30-fold decrease in the catalytic efficiency.
K242 (= K243) modified: N6-succinyllysine
K250 (= K250) modified: N6-acetyllysine; alternate; modified: N6-succinyllysine; alternate
P258 (= P258) mutation to A: Important decrease in affinity and catalytic efficiency. Reduced thermal stability.; mutation to G: Important decrease in affinity and catalytic efficiency.
P264 (= P264) mutation to A: Important decrease in affinity and catalytic efficiency.; mutation to G: Important decrease in affinity and catalytic efficiency.
L276 (≠ F276) mutation to A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-85.
K277 (= K277) modified: N6-succinyllysine
K285 (= K285) modified: N6-acetyllysine
K293 (= K293) modified: N6-succinyllysine
K331 (= K331) modified: N6-succinyllysine
K346 (= K346) modified: N6-succinyllysine
K354 (≠ Q354) modified: N6-acetyllysine; alternate; modified: N6-succinyllysine; alternate
R363 (= R363) mutation to A: It does not bind serine and glycine and shows no activity with serine as the substrate.; mutation to K: Exhibits only 0.03% of the catalytic activity of the wild-type and a 15-fold reduction in affinity for glycine and serine.
R372 (= R372) mutation to A: No significant difference compared to the wild-type.; mutation to K: No significant difference compared to the wild-type.
K375 (= K375) modified: N6-acetyllysine

1eqbA X-ray crystal structure at 2.7 angstroms resolution of ternary complex between the y65f mutant of e-coli serine hydroxymethyltransferase, glycine and 5-formyl tetrahydrofolate (see paper)
69% identity, 99% coverage: 2:416/418 of query aligns to 1:415/416 of 1eqbA

query
sites
1eqbA

F

L

S

K

Q

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K

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Q

G

G

P

P

L

L

M

M

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

L

K

K

E

E

A

A

M

M

E

E

P

P

E

E

F

F

K

K

V

T

Y

Y

Q

Q

V

V

I

A

K

K

N

N

A

A

Q

K

A

A

M

M

A

V

K

E

V

V

F

F

V

L

D

E

R

R

G

G

F

Y

D

K

V

V

S

S

G

G

T

T

D

D

N

N

H

H

L

L

M

F

L

L

V

V

S

D

L

L

I

V

P

D

K

K

G

N

I

L

T

T

G

G

K

K

A

E

A

A

D

D

A

A

L

L

G

G

K

R

A

A

H

N

I

I

T

T

V

V

N

N

K

K

N
|
N

A

S

V

V

P

P

N

N

D

D

P

P

Q

K

S
|
S

P
|
P

F
|
F

V

V

T

T

S

S

G

G

I

I

R
|
R

V

V

G

G

T

T

P

P

A

A

P

I

T

T

T

R

R

R

G

G

F

F

K

K

E

E

A

A

Q

E

M

A

I

K

D

E

V

L

A

A

H

G

W

W

M

M

C

C

D

D

V

V

M

L

E

D

N

S

I

I

D

N

D

D

E

E

N

A

V

V

A

I

A

E

A

R

V

I

R

K

E

G

K

K

V

V

H

L

K

D

L

I

C

C

A

A

Q

R

F

Y

P

P

V

V

Y

Y

active site: Y54 (= Y55), E56 (= E57), D199 (= D201), T225 (= T227), K228 (= K230), R234 (= R236)
binding N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid: E56 (= E57), Y63 (= Y64), L120 (= L121), G123 (= G124), G124 (= G125), H125 (= H126), L126 (= L127), S174 (= S176), N346 (= N347), S354 (= S355), P355 (= P356), F356 (= F357)
binding glycine: S34 (= S35), Y54 (= Y55), F64 (≠ Y65), H202 (= H204), K228 (= K230), R362 (= R363)
binding pyridoxal-5'-phosphate: S96 (= S97), G97 (= G98), S98 (= S99), H125 (= H126), F173 (= F175), S174 (= S176), D199 (= D201), H202 (= H204), H227 (= H229), K228 (= K230)

4n0wA X-ray crystal structure of a serine hydroxymethyltransferase from burkholderia cenocepacia with covalently attached pyridoxal phosphate
64% identity, 100% coverage: 1:416/418 of query aligns to 2:415/416 of 4n0wA

query
sites
4n0wA

M

M

F

F

S

D

Q

R

A

A

M

Q

-

S

T

T

I

I

A

A

G

N

F

V

D

D

D

P

E

E

L

I

F

F

Q

A

A

A

L

I

E

E

E

Q

E

E

R

N

R

R

Q

Q

E

E

N

D

H

H

I

I

E

E

L

L

I

I

A

A

S

S

E

E

N

N

Y

Y

A

T

S

S

P

P

R

A

V

V

L

M

E

A

A

A

Q

Q

G

G

T

S

L

Q

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E
|
E

G

G

Y

Y

P

P

G

G

K

K

R

R

Y

Y

G

G

C

C

E

E

F

Y

V

V

D

D

K

V

A

V

E

E

Q

Q

L

L

A

A

I

I

D

D

R

R

A

V

K

K

A

Q

L

L

F

F

G

G

A

A

D

E

Y

A

A

A

N

N

V

V

Q

Q

A

P

H

N

S
|
S

G
|
G

S
|
S

Q

Q

A

A

N

N

M

Q

A

G

V

V

F

F

M

F

A

A

L

M

I

L

Q

K

P

P

G

G

D

D

T

T

I

I

L

M

G

G

L

M

S

S

L

L

A

A

D

H

G

G

H
|
H

L

L

T

T

H

H

G

G

A

S

K

P

P

V

N

N

F

M

S

S

G

G

K

K

I

W

Y

F

R

N

A

V

I

V

Q

S

Y

Y

G

G

L

L

H

N

P

-

K

E

T

N

G

E

E

D

I

I

D

D

Y

Y

E

D

Q

A

V

A

E

E

A

K

L

L

A

A

L

N

E

E

H

H

K

K

P

P

K

K

L

L

I

I

V

V

A

A

G

G

F

A

S

S

A

A

Y

F

S

A

R

L

I

K

W

I

D

D

W

F

Q

E

R

R

F

L

R

A

E

K

I

I

A

A

D

K

K

S

V

V

G

G

A

A

Y

Y

F

L

V

M

V

V

D
|
D

M

M

A
|
A

H
|
H

V

Y

A

A

G

G

L

L

V

I

A

A

G

G

L

V

Y

Y

P

P

N

N

P

P

V

V

P

P

I

H

A

A

D

D

V

F

V

V

T

T

S

T

T
|
T

T

T

H

H

K
|
K

S

S

L

L

C

R

G

G

P

P

R
|
R

G

G

L

V

I

I

L

L

C

M

K

K

S

A

N

-

P

-

E

E

L

Y

E

E

K

K

K

P

F

I

D

N

S

S

N

A

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

M

H

H

V

V

I

I

A

A

K

K

A

A

V

V

A

A

F

F

K

K

E

E

A

A

M

L

E

S

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

Q

Q

K

V

V

I

V

K

E

N

N

A

A

Q

R

A

V

M

L

A

A

K

E

V

T

F

L

V

V

D

K

R

R

G

G

F

L

D

R

V

I

V

V

S

S

G

G

G

R

T

T

D

E

N

S

H

H

L

V

M

M

L

L

V

V

S

D

L

L

I

R

P

A

K

K

G

H

I

I

T

T

G

G

K

K

A

A

D

E

A

A

L

L

G

G

K

A

A

A

H

H

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

N

D

D

P

P

Q

E

S

K

P

P

F

F

V

V

T

T

S

S

G

G

I

I

R

R

V

L

G

G

T

S

P

P

A

A

P

M

T

T

R

R

G

G

F

F

K

G

E

P

A

A

Q

E

M

A

I

E

D

Q

V

V

A

G

H

N

W

L

M

I

C

A

D

D

V

V

M

L

E

E

N

N

I

P

D

E

D

D

E

A

N

A

V

T

A

I

A

E

A

R

V

V

R

R

E

A

K

Q

V

V

H

A

K

E

L

L

C

T

A

K

Q

R

F

F

P

P

V

V

Y

Y

active site: Y57 (= Y55), E59 (= E57), D202 (= D201), T228 (= T227), K231 (= K230), R237 (= R236)
binding pyridoxal-5'-phosphate: S99 (= S97), G100 (= G98), S101 (= S99), H128 (= H126), D202 (= D201), A204 (= A203), H205 (= H204), K231 (= K230)

4otlA X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and glycine
65% identity, 98% coverage: 7:416/418 of query aligns to 2:408/409 of 4otlA

query
sites
4otlA

T

T

I

I

A

A

G

N

F

V

D

D

D

P

E

E

L

I

F

F

Q

A

A

A

L

I

E

E

E

Q

E

E

R

N

R

R

Q

Q

E

E

N

D

H

H

I

I

E

E

L

L

I

I

A

A

S
|
S

E

E

N

N

Y

Y

A

T

S

S

P

P

R

A

V

V

L

M

E

A

A

A

Q

Q

G

G

T

S

L

Q

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E
|
E

G

G

Y

Y

P

P

G

G

K

K

R

R

Y

Y

Y
|
Y

G

G

C

C

E

E

F

Y

V

V

D

D

K

V

A

V

E

E

Q

Q

L

L

A

A

I

I

D

D

R

R

A

V

K

K

A

Q

L

L

F

F

G

G

A

A

D

E

Y

A

A

A

N

N

V

V

Q

Q

A

P

H

N

S
|
S

G
|
G

S
|
S

Q

Q

A

A

N

N

M

Q

A

G

V

V

F

F

M

F

A

A

L

M

I

L

Q

K

P

P

G

G

D

D

T

T

I

I

L

M

G

G

L

M

S

S

L

L

A

A

D

H

G

G

H
|
H

L

L

T

T

H

H

G

G

A

S

K

P

P

V

N

N

F

M

S

S

G

G

K

K

I

W

Y

F

R

N

A

V

I

V

Q

S

Y

Y

G

G

L

L

H

N

P

-

K

E

T

N

G

E

E

D

I

I

D

D

Y

Y

E

D

Q

A

V

A

E

E

A

K

L

L

A

A

L

N

E

E

H

H

K

K

P

P

K

K

L

L

I

I

V

V

A

A

G

G

F

A

S
|
S

A

A

Y

F

S

A

R

L

I

K

W

I

D

D

W

F

Q

E

R

R

F

L

R

A

E

K

I

I

A

A

D

K

K

S

V

V

G

G

A

A

Y

Y

F

L

V

M

V

V

D
|
D

M

M

A
|
A

H
|
H

V

Y

A

A

G

G

L

L

V

I

A

A

G

G

L

V

Y

Y

P

P

N

N

P

P

V

V

P

P

I

H

A

A

D

D

V

F

V

V

T

T

S

T

T
|
T

T

T

H

H

K
|
K

S

S

L

L

C

R

G

G

P

P

R
|
R

G

G

L

V

I

I

L

L

C

M

K

K

S

A

N

-

P

-

E

E

L

Y

E

E

K

K

K

P

F

I

D

N

S

S

N

A

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

M

H

H

V

V

I

I

A

A

K

K

A

A

V

V

A

A

F

F

K

K

E

E

A

A

M

L

E

S

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

Q

Q

K

V

V

I

V

K

E

N

N

A

A

Q

R

A

V

M

L

A

A

K

E

V

T

F

L

V

V

D

K

R

R

G

G

F

L

D

R

V

I

V

V

S

S

G

G

G

R

T

T

D

E

N

S

H

H

L

V

M

M

L

L

V

V

S

D

L

L

I

R

P

A

K

K

G

H

I

I

T

T

G

G

K

K

A

A

D

E

A

A

L

L

G

G

K

A

A

A

H

H

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

N

D

D

P

P

Q

E

S

K

P

P

F

F

V

V

T

T

S

S

G

G

I

I

R
|
R

V

L

G

G

T

S

P

P

A

A

P

M

T

T

R

R

G

G

F

F

K

G

E

P

A

A

Q

E

M

A

I

E

D

Q

V

V

A

G

H

N

W

L

M

I

C

A

D

D

V

V

M

L

E

E

N

N

I

P

D

E

D

D

E

A

N

A

V

T

A

I

A

E

A

R

V

V

R

R

E

A

K

Q

V

V

H

A

K

E

L

L

C

T

A

K

Q

R

F

F

P

P

V

V

Y

Y

active site: Y50 (= Y55), E52 (= E57), D195 (= D201), T221 (= T227), K224 (= K230), R230 (= R236)
binding glycine: S30 (= S35), Y50 (= Y55), Y60 (= Y65), H121 (= H126), K224 (= K230), R355 (= R363)
binding pyridoxal-5'-phosphate: S92 (= S97), G93 (= G98), S94 (= S99), H121 (= H126), S170 (= S176), D195 (= D201), A197 (= A203), H198 (= H204), K224 (= K230)

4ot8A X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and serine
65% identity, 98% coverage: 7:416/418 of query aligns to 7:413/414 of 4ot8A

query
sites
4ot8A

T

T

I

I

A

A

G

N

F

V

D

D

D

P

E

E

L

I

F

F

Q

A

A

A

L

I

E

E

E

Q

E

E

R

N

R

R

Q

Q

E

E

N

D

H

H

I

I

E

E

L

L

I

I

A

A

S
|
S

E

E

N

N

Y

Y

A

T

S

S

P

P

R

A

V

V

L

M

E

A

A

A

Q

Q

G

G

T

S

L

Q

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E
|
E

G

G

Y

Y

P

P

G

G

K

K

R

R

Y

Y

Y
|
Y

G

G

C

C

E

E

F

Y

V

V

D

D

K

V

A

V

E

E

Q

Q

L

L

A

A

I

I

D

D

R

R

A

V

K

K

A

Q

L

L

F

F

G

G

A

A

D

E

Y

A

A

A

N

N

V

V

Q

Q

A

P

H

N

S
|
S

G
|
G

S
|
S

Q

Q

A

A

N

N

M

Q

A

G

V

V

F

F

M

F

A

A

L

M

I

L

Q

K

P

P

G

G

D

D

T

T

I

I

L

M

G

G

L

M

S

S

L

L

A

A

D

H

G

G

H
|
H

L

L

T

T

H

H

G

G

A

S

K

P

P

V

N

N

F

M

S

S

G

G

K

K

I

W

Y

F

R

N

A

V

I

V

Q

S

Y

Y

G

G

L

L

H

N

P

-

K

E

T

N

G

E

E

D

I

I

D

D

Y

Y

E

D

Q

A

V

A

E

E

A

K

L

L

A

A

L

N

E

E

H

H

K

K

P

P

K

K

L

L

I

I

V

V

A

A

G

G

F

A

S

S

A

A

Y

F

S

A

R

L

I

K

W

I

D

D

W

F

Q

E

R

R

F

L

R

A

E

K

I

I

A

A

D

K

K

S

V

V

G

G

A

A

Y

Y

F

L

V

M

V

V

D
|
D

M

M

A
|
A

H
|
H

V

Y

A

A

G

G

L

L

V

I

A

A

G

G

L

V

Y

Y

P

P

N

N

P

P

V

V

P

P

I

H

A

A

D

D

V

F

V

V

T

T

S

T

T
|
T

T

T

H

H

K
|
K

S

S

L

L

C

R

G

G

P

P

R
|
R

G

G

L

V

I

I

L

L

C

M

K

K

S

A

N

-

P

-

E

E

L

Y

E

E

K

K

K

P

F

I

D

N

S

S

N

A

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

M

H

H

V

V

I

I

A

A

K

K

A

A

V

V

A

A

F

F

K

K

E

E

A

A

M

L

E

S

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

Q

Q

K

V

V

I

V

K

E

N

N

A

A

Q

R

A

V

M

L

A

A

K

E

V

T

F

L

V

V

D

K

R

R

G

G

F

L

D

R

V

I

V

V

S

S

G

G

G

R

T

T

D

E

N

S

H

H

L

V

M

M

L

L

V

V

S

D

L

L

I

R

P

A

K

K

G

H

I

I

T

T

G

G

K

K

A

A

D

E

A

A

L

L

G

G

K

A

A

A

H

H

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

N

D

D

P

P

Q

E

S

K

P

P

F

F

V

V

T

T

S

S

G

G

I

I

R
|
R

V

L

G

G

T

S

P

P

A

A

P

M

T

T

R

R

G

G

F

F

K

G

E

P

A

A

Q

E

M

A

I

E

D

Q

V

V

A

G

H

N

W

L

M

I

C

A

D

D

V

V

M

L

E

E

N

N

I

P

D

E

D

D

E

A

N

A

V

T

A

I

A

E

A

R

V

V

R

R

E

A

K

Q

V

V

H

A

K

E

L

L

C

T

A

K

Q

R

F

F

P

P

V

V

Y

Y

active site: Y55 (= Y55), E57 (= E57), D200 (= D201), T226 (= T227), K229 (= K230), R235 (= R236)
binding pyridoxal-5'-phosphate: S97 (= S97), G98 (= G98), S99 (= S99), H126 (= H126), D200 (= D201), A202 (= A203), H203 (= H204), K229 (= K230)
binding serine: S35 (= S35), E57 (= E57), Y65 (= Y65), H126 (= H126), H203 (= H204), R360 (= R363)

Q5SI56 Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
62% identity, 97% coverage: 12:415/418 of query aligns to 8:406/407 of Q5SI56

query
sites
Q5SI56

D

D

D

E

E

A

L

L

F

F

Q

E

A

L

L

I

E

A

E

L

E

E

R

E

R

K

R

R

Q

Q

E

R

N

E

H

G

I

L

E

E

L

L

I

I

A

A

S

S

E

E

N

N

Y

F

A

V

S

S

P

K

R

Q

V

V

L

R

E

E

A

A

Q

V

G

G

T

S

L

V

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E

E

G

G

Y

Y

P

P

G

G

K

A

R

R

Y

Y

G

G

C

C

E

E

F

V

V

I

D

D

K

R

A

V

E

E

Q

S

L

L

A

A

I

I

D

E

R

R

A

A

K

K

A

A

L

L

F

F

G

G

A

A

D

A

Y

W

A

A

N

N

V

V

Q

Q

A

P

H

H

S

S

G
|
G

S
|
S

Q

Q

A

A

N

N

M

M

A

A

V

V

F

Y

M

M

A

A

L

L

I

M

Q

E

P

P

G

G

D

D

T

T

I

L

L

M

G

G

L

M

S

D

L

L

A

A

D

A

G

G

H

H

L

L

T

T

H

H

G

G

A

S

K

R

P

V

N

N

F

F

S

S

G

G

K

K

I

L

Y

Y

R

K

A

V

I

V

Q

S

Y

Y

G

G

L

V

H

R

P

P

K

D

T

T

G

E

E

L

I

I

D

D

Y

L

E

E

Q

E

V

V

E

R

A

R

L

L

A

A

L

L

E

E

H

H

K

R

P

P

K

K

L

V

I

I

V

V

A

A

G

G

F

A

S
|
S

A

A

Y

Y

S

P

R

R

I

F

W

W

D

D

W

F

Q

K

R

A

F

F

R

R

E

E

I

I

A

A

D

D

K

E

V

V

G

G

A

A

Y

Y

F

L

V

V

D

D

M

M

A

A

H
|
H

V

F

A

A

G

G

L

L

V

V

A

A

G

G

L

L

Y

H

P

P

N

N

P

P

V

L

P

P

I

Y

A

A

D

H

V

V

T

T

S

S

T

T

H
|
H

K
|
K

S

T

L

L

C

R

G

G

P

P

R

R

G

G

L

L

I

I

L

L

C

S

K

-

S

N

N

D

P

P

E

E

L

L

E

G

K

K

K

R

F

I

D

D

S

K

N

L

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

G
|
G

P

P

L

L

M

E

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

F

K

F

E

E

A

A

M

L

E

Q

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

S

Q

R

Q

L

V

V

I

V

K

E

N

N

A

A

Q

K

A

R

M

L

A

A

K

E

V

E

F

L

V

A

D

R

R

R

G

G

F

Y

D

R

V

I

V

V

S

T

G

G

T

T

D

D

N

N

H

H

L

L

M

F

L

L

V

V

S

D

L

L

I

R

P

P

K

K

G

G

I

L

T

T

G

G

K

K

A

E

A

A

D

E

A

E

A

R

L

L

G

D

K

A

A

V

H

G

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

F

D

D

P

P

Q

K

S

P

P

P

F

R

V

V

T

T

S

S

G

G

I

I

R

R

V

I

G

G

T

T

P

P

A

A

P

I

T

T

R

R

G

G

F

F

K

T

E

P

A

E

Q

E

M

M

I

P

D

L

V

V

A

A

H

-

W

-

M

-

C

-

D

E

V

L

M

I

E

D

N

R

I

A

D

L

E

E

N

G

V

P

A

S

A

E

A

A

V

L

R

R

E

E

K

E

V

V

H

R

K

R

L

L

C

A

A

L

Q

A

F

H

P

P

V

M

Y51 (= Y55) binding pyridoxal 5'-phosphate
GS 94:95 (= GS 98:99) binding pyridoxal 5'-phosphate
S172 (= S176) binding pyridoxal 5'-phosphate
H200 (= H204) binding pyridoxal 5'-phosphate
H225 (= H229) binding pyridoxal 5'-phosphate
K226 (= K230) modified: N6-(pyridoxal phosphate)lysine
G258 (= G263) binding pyridoxal 5'-phosphate

8suiB Joint x-ray/neutron structure of thermus thermophilus serine hydroxymethyltransferase (tthshmt) in internal aldimine state with l- ser bound in a pre-michalis complex (see paper)
62% identity, 97% coverage: 12:415/418 of query aligns to 3:401/402 of 8suiB

query
sites
8suiB

D

D

D

E

E

A

L

L

F

F

Q

E

A

L

L

I

E

A

E

L

E

E

R

E

R

K

R

R

Q

Q

E

R

N

E

H

G

I

L

E

E

L

L

I

I

A

A

S

S

E

E

N

N

Y

F

A

V

S

S

P

K

R

Q

V

V

L

R

E

E

A

A

Q

V

G

G

T

S

L

V

L

L

T

T

N

N

K

K

Y

Y

A

A

E

E

G

G

Y

Y

P

P

G

G

K

A

R

R

Y
|
Y

G

G

C

C

E

E

F

V

V

I

D

D

K

R

A

V

E

E

Q

S

L

L

A

A

I

I

D

E

R

R

A

A

K

K

A

A

L

L

F

F

G

G

A

A

D

A

Y

W

A

A

N

N

V

V

Q

Q

A

P

H

H

S

S

G

G

S

S

Q

Q

A

A

N

N

M

M

A

A

V

V

F

Y

M

M

A

A

L

L

I

M

Q

E

P

P

G

G

D

D

T

T

I

L

L

M

G

G

L

M

S

D

L

L

A

A

D

A

G

G

H

H

L

L

T

T

H

H

G

G

A

S

K

R

P

V

N

N

F

F

S

S

G

G

K

K

I

L

Y

Y

R

K

A

V

I

V

Q

S

Y

Y

G

G

L

V

H

R

P

P

K

D

T

T

G

E

E

L

I

I

D

D

Y

L

E

E

Q

E

V

V

E

R

A

R

L

L

A

A

L

L

E

E

H

H

K

R

P

P

K

K

L

V

I

I

V

V

A

A

G

G

F

A

S

S

A

A

Y

Y

S

P

R

R

I

F

W

W

D

D

W

F

Q

K

R

A

F

F

R

R

E

E

I

I

A

A

D

D

K

E

V

V

G

G

A

A

Y

Y

F

L

V

V

D

D

M

M

A

A

H

H

V

F

A

A

G

G

L

L

V

V

A

A

G

G

L

L

Y

H

P

P

N

N

P

P

V

L

P

P

I

Y

A

A

D

H

V

V

T

T

S

S

T

T

H

H

K

K

S

T

L

L

C

R

G

G

P

P

R

R

G

G

L

L

I

I

L

L

C

S

K

-

S

N

N

D

P

P

E

E

L

L

E

G

K

K

K

R

F

I

D

D

S

K

N

L

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

E

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

F

K

F

E

E

A

A

M

L

E

Q

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

S

Q

R

Q

L

V

V

I

V

K

E

N

N

A

A

Q

K

A

R

M

L

A

A

K

E

V

E

F

L

V

A

D

R

R

R

G

G

F

Y

D

R

V

I

V

V

S

T

G

G

T

T

D

D

N

N

H

H

L

L

M

F

L

L

V

V

S

D

L

L

I

R

P

P

K

K

G

G

I

L

T

T

G

G

K

K

A

E

A

A

D

E

A

E

A

R

L

L

G

D

K

A

A

V

H

G

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

F

D

D

P

P

Q

K

S

P

P

P

F

R

V

V

T

T

S

S

G

G

I

I

R

R

V

I

G

G

T

T

P

P

A

A

P

I

T

T

R

R

G

G

F

F

K

T

E

P

A

E

Q

E

M

M

I

P

D

L

V

V

A

A

H

-

W

-

M

-

C

-

D

E

V

L

M

I

E

D

N

R

I

A

D

L

E

E

N

G

V

P

A

S

A

E

A

A

V

L

R

R

E

E

K

E

V

V

H

R

K

R

L

L

C

A

A

L

Q

A

F

H

P

P

V

M

binding serine: Y55 (= Y64), Y56 (= Y65)

8ssyA Room-temperature x-ray structure of thermus thermophilus serine hydroxymethyltransferase (shmt) bound with d-ser in a pseudo- michaelis complex (see paper)
62% identity, 97% coverage: 12:415/418 of query aligns to 3:401/402 of 8ssyA

query
sites
8ssyA

D

D

D

E

E

A

L

L

F

F

Q

E

A

L

L

I

E

A

E

L

E

E

R

E

R

K

R

R

Q

Q

E

R

N

E

H

G

I

L

E

E

L

L

I

I

A

A

S
|
S

E

E

N

N

Y

F

A

V

S

S

P

K

R

Q

V

V

L

R

E

E

A

A

Q

V

G

G

T

S

L

V

L

L

T

T

N

N

K

K

Y

Y

A

A

E

E

G

G

Y

Y

P

P

G

G

K

A

R

R

Y

Y

G

G

C

C

E

E

F

V

V

I

D

D

K

R

A

V

E

E

Q

S

L

L

A

A

I

I

D

E

R

R

A

A

K

K

A

A

L

L

F

F

G

G

A

A

D

A

Y

W

A

A

N

N

V

V

Q

Q

A

P

H

H

S

S

G

G

S

S

Q

Q

A

A

N

N

M

M

A

A

V

V

F

Y

M

M

A

A

L

L

I

M

Q

E

P

P

G

G

D

D

T

T

I

L

L

M

G

G

L

M

S

D

L

L

A

A

D

A

G

G

H

H

L

L

T

T

H

H

G

G

A

S

K

R

P

V

N

N

F

F

S

S

G

G

K

K

I

L

Y

Y

R

K

A

V

I

V

Q

S

Y

Y

G

G

L

V

H

R

P

P

K

D

T

T

G

E

E

L

I

I

D

D

Y

L

E

E

Q

E

V

V

E

R

A

R

L

L

A

A

L

L

E

E

H

H

K

R

P

P

K

K

L

V

I

I

V

V

A

A

G

G

F

A

S

S

A

A

Y

Y

S

P

R

R

I

F

W

W

D

D

W

F

Q

K

R

A

F

F

R

R

E

E

I

I

A

A

D

D

K

E

V

V

G

G

A

A

Y

Y

F

L

V

V

D

D

M

M

A

A

H
|
H

V

F

A

A

G

G

L

L

V

V

A

A

G

G

L

L

Y

H

P

P

N

N

P

P

V

L

P

P

I

Y

A

A

D

H

V

V

T

T

S

S

T

T

H

H

K
|
K

S

T

L

L

C

R

G

G

P

P

R

R

G

G

L

L

I

I

L

L

C

S

K

-

S

N

N

D

P

P

E

E

L

L

E

G

K

K

K

R

F

I

D

D

S

K

N

L

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

E

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

F

K

F

E

E

A

A

M

L

E

Q

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

S

Q

R

Q

L

V

V

I

V

K

E

N

N

A

A

Q

K

A

R

M

L

A

A

K

E

V

E

F

L

V

A

D

R

R

R

G

G

F

Y

D

R

V

I

V

V

S

T

G

G

T

T

D

D

N

N

H

H

L

L

M

F

L

L

V

V

S

D

L

L

I

R

P

P

K

K

G

G

I

L

T

T

G

G

K

K

A

E

A

A

D

E

A

E

A

R

L

L

G

D

K

A

A

V

H

G

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

F

D

D

P

P

Q

K

S

P

P

P

F

R

V

V

T

T

S

S

G

G

I

I

R
|
R

V

I

G

G

T

T

P

P

A

A

P

I

T

T

R

R

G

G

F

F

K

T

E

P

A

E

Q

E

M

M

I

P

D

L

V

V

A

A

H

-

W

-

M

-

C

-

D

E

V

L

M

I

E

D

N

R

I

A

D

L

E

E

N

G

V

P

A

S

A

E

A

A

V

L

R

R

E

E

K

E

V

V

H

R

K

R

L

L

C

A

A

L

Q

A

F

H

P

P

V

M

binding d-serine: S26 (= S35), H195 (= H204), K221 (= K230), R353 (= R363)

2dkjA Crystal structure of t.Th.Hb8 serine hydroxymethyltransferase
62% identity, 97% coverage: 12:415/418 of query aligns to 3:401/402 of 2dkjA

query
sites
2dkjA

D

D

D

E

E

A

L

L

F

F

Q

E

A

L

L

I

E

A

E

L

E

E

R

E

R

K

R

R

Q

Q

E

R

N

E

H

G

I

L

E

E

L

L

I

I

A

A

S

S

E

E

N

N

Y

F

A

V

S

S

P

K

R

Q

V

V

L

R

E

E

A

A

Q

V

G

G

T

S

L

V

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E
|
E

G

G

Y

Y

P

P

G

G

K

A

R

R

Y

Y

G

G

C

C

E

E

F

V

V

I

D

D

K

R

A

V

E

E

Q

S

L

L

A

A

I

I

D

E

R

R

A

A

K

K

A

A

L

L

F

F

G

G

A

A

D

A

Y

W

A

A

N

N

V

V

Q

Q

A

P

H

H

S
|
S

G
|
G

S
|
S

Q

Q

A

A

N

N

M

M

A

A

V

V

F

Y

M

M

A

A

L

L

I

M

Q

E

P

P

G

G

D

D

T

T

I

L

L

M

G

G

L

M

S

D

L

L

A

A

D

A

G

G

H
|
H

L

L

T

T

H

H

G

G

A

S

K

R

P

V

N

N

F

F

S

S

G

G

K

K

I

L

Y

Y

R

K

A

V

I

V

Q

S

Y

Y

G

G

L

V

H

R

P

P

K

D

T

T

G

E

E

L

I

I

D

D

Y

L

E

E

Q

E

V

V

E

R

A

R

L

L

A

A

L

L

E

E

H

H

K

R

P

P

K

K

L

V

I

I

V

V

A

A

G

G

F

A

S
|
S

A

A

Y

Y

S

P

R

R

I

F

W

W

D

D

W

F

Q

K

R

A

F

F

R

R

E

E

I

I

A

A

D

D

K

E

V

V

G

G

A

A

Y

Y

F

L

V

V

D
|
D

M

M

A
|
A

H

H

V

F

A

A

G

G

L

L

V

V

A

A

G

G

L

L

Y

H

P

P

N

N

P

P

V

L

P

P

I

Y

A

A

D

H

V

V

T

T

S

S

T
|
T

T

T

H
|
H

K
|
K

S

T

L

L

C

R

G

G

P

P

R
|
R

G

G

L

L

I

I

L

L

C

S

K

-

S

N

N

D

P

P

E

E

L

L

E

G

K

K

K

R

F

I

D

D

S

K

N

L

I

I

F

F

P

P

G

G

I

I

Q

Q

G

G

P

P

L

L

M

E

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

F

K

F

E

E

A

A

M

L

E

Q

P

P

E

E

F

F

K

K

V

E

Y

Y

Q

S

Q

R

Q

L

V

V

I

V

K

E

N

N

A

A

Q

K

A

R

M

L

A

A

K

E

V

E

F

L

V

A

D

R

R

R

G

G

F

Y

D

R

V

I

V

V

S

T

G

G

T

T

D

D

N

N

H

H

L

L

M

F

L

L

V

V

S

D

L

L

I

R

P

P

K

K

G

G

I

L

T

T

G

G

K

K

A

E

A

A

D

E

A

E

A

R

L

L

G

D

K

A

A

V

H

G

I

I

T

T

V

V

N

N

K

K

N

N

A

A

V

I

P

P

N

F

D

D

P

P

Q

K

S

P

P

P

F

R

V

V

T

T

S

S

G

G

I

I

R

R

V

I

G

G

T

T

P

P

A

A

P

I

T

T

R

R

G

G

F

F

K

T

E

P

A

E

Q

E

M

M

I

P

D

L

V

V

A

A

H

-

W

-

M

-

C

-

D

E

V

L

M

I

E

D

N

R

I

A

D

L

E

E

N

G

V

P

A

S

A

E

A

A

V

L

R

R

E

E

K

E

V

V

H

R

K

R

L

L

C

A

A

L

Q

A

F

H

P

P

V

M

active site: Y46 (= Y55), E48 (= E57), D192 (= D201), T218 (= T227), K221 (= K230), R227 (= R236)
binding pyridoxal-5'-phosphate: S88 (= S97), G89 (= G98), S90 (= S99), H117 (= H126), S167 (= S176), D192 (= D201), A194 (= A203), H220 (= H229), K221 (= K230)

6ymfA Crystal structure of serine hydroxymethyltransferase from aphanothece halophytica in the plp-serine external aldimine state (see paper)
58% identity, 95% coverage: 19:416/418 of query aligns to 18:414/418 of 6ymfA

query
sites
6ymfA

L

M

E

Q

E

K

E

E

R

L

R

Q

R

R

Q

Q

E

R

N

E

H

H

I

L

E

E

L

L

I

I

A

A

S
|
S

E

E

N

N

Y

F

A

T

S

S

P

P

R

A

V

V

L

M

E

A

A

T

Q

Q

G

G

T

S

L

V

L

L

T

T

N

N

K

K

Y
|
Y

A

A

E
|
E

G

G

Y

L

P

P

G

K

K

K

R

R

Y

Y

G

G

C

C

E

E

F

F

V

I

D

D

K

E

A

I

E

E

Q

Q

L

V

A

A

I

I

D

D

R

R

A

A

K

K

A

E

L

L

F

F

G

G

A

A

D

A

Y

S

A

A

N

N

V

V

Q

Q

A

P

H

H

S
|
S

G
|
G

S
x
A

Q

Q

A

A

N

N

M

F

A

A

V

V

F

F

M

L

A

T

L

L

I

L

Q

K

P

P

G

G

D

D

T

K

I

I

L

M

G

G

L

M

S

D

L

L

A

S

D

H

G

G

H
|
H

L

L

T

T

H

H

G

G

A

S

K

P

P

A

N

N

F

V

S

S

G

G

K

K

I

W

Y

F

R

E

A

A

I

V

Q

H

Y

Y

G

G

L

V

H

S

P

Q

K

E

T

T

G

E

E

Q

I

L

D

D

Y

Y

E

D

Q

H

V

I

E

L

A

E

L

V

A

A

L

R

E

Q

H

E

K

R

P

P

K

K

L

L

I

I

V

I

A

C

G

G

F

Y

S
|
S

A

A

Y

Y

S

P

R

R

I

I

W

I

D

N

W

F

Q

E

R

K

F

F

R

R

E

A

I

I

A

A

D

D

K

E

V

V

G

G

A

A

Y

Y

F

L

V

L

V

A

D
|
D

M

I

A
|
A

H
|
H

V

I

A

A

G

G

L

L

V

V

A

A

A

S

G

G

L

H

Y

H

P

P

N

N

P

P

V

V

P

P

I

H

A

C

D

D

V

V

T

T

S

T

T
|
T

T

T

H

H

K
|
K

S

T

L

L

C

R

G

G

P

P

R
|
R

G

G

L

L

I

I

L

L

C

T

K

R

S

-

N

D

P

P

E

E

L

L

E

G

K

K

F

F

D

N

S

K

N

S

I

V

F

F

P

P

G

G

I

T

Q

Q

G

G

P

P

L

L

M

E

H

H

V

V

I

I

A

A

A

G

K

K

A

A

V

V

A

A

F

F

K

G

E

E

A

A

M

L

E

K

P

P

E

E