SitesBLAST

P13009 Methionine synthase; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12-dependent; MS; EC 2.1.1.13 from Escherichia coli (strain K12) (see 5 papers)
31% identity, 69% coverage: 34:179/211 of query aligns to 689:835/1227 of P13009

query
sites
P13009

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A

E694 (= E39) binding methylcob(III)alamin
GDVHD 756:760 (= GDVHD 98:102) binding methylcob(III)alamin
D757 (= D99) mutation to E: Decreases activity by about 70%.; mutation to N: Decreases activity by about 45%.
H759 (= H101) binding axial binding residue; mutation to G: Loss of catalytic activity.
S804 (= S146) binding methylcob(III)alamin
T808 (= T150) binding methylcob(III)alamin
S810 (≠ A152) mutation to A: Decreases activity by about 40%.

Sites not aligning to the query:

1 modified: Initiator methionine, Removed
247 binding Zn(2+)
310 binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
311 binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
860 binding methylcob(III)alamin
946 binding S-adenosyl-L-methionine
1134 binding S-adenosyl-L-methionine
1189:1190 binding S-adenosyl-L-methionine

1bmtA How a protein binds b12: a 3.O angstrom x-ray structure of the b12- binding domains of methionine synthase (see paper)
31% identity, 69% coverage: 34:178/211 of query aligns to 39:184/246 of 1bmtA

query
sites
1bmtA

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active site: D107 (= D99), H109 (= H101), S160 (≠ A152)
binding co-methylcobalamin: E44 (= E39), M48 (≠ R42), M51 (≠ T45), G55 (= G49), L65 (≠ V59), V68 (≠ L62), D107 (= D99), V108 (= V100), H109 (= H101), D110 (= D102), I111 (= I103), I115 (= I107), G152 (≠ S144), L153 (= L145), S154 (= S146), L156 (= L148), I157 (≠ L149), T158 (= T150), G183 (= G177), G184 (= G178)

Sites not aligning to the query:

binding co-methylcobalamin: 185, 207, 209, 210

2i2xB Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri (see paper)
28% identity, 90% coverage: 11:199/211 of query aligns to 46:232/258 of 2i2xB

query
sites
2i2xB

A

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N

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A

active site: D134 (= D99), H136 (= H101), T187 (≠ A152)
binding 5-hydroxybenzimidazolylcob(iii)amide: G133 (= G98), D134 (= D99), V135 (= V100), H136 (= H101), D137 (= D102), I138 (= I103), G139 (= G104), V143 (= V108), T179 (≠ S144), T181 (≠ S146), L183 (= L148), M184 (≠ L149), T185 (= T150), A208 (≠ V175), G210 (= G177), G211 (= G178), G212 (= G179), G228 (≠ A195), E229 (≠ D196), E230 (≠ D197), A231 (= A198)

Q46EH4 Methanol--corrinoid protein; Methanol:corrinoid methyltransferase 1 subunit of 27 kDa; MT1 subunit 27 kDa from Methanosarcina barkeri (strain Fusaro / DSM 804) (see paper)
28% identity, 90% coverage: 11:199/211 of query aligns to 46:232/258 of Q46EH4

query
sites
Q46EH4

A

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H129 (≠ G94) mutation to K: Does not affect cobalamin-binding.
H136 (= H101) mutation H->G,K: Abolishes cobalamin-binding.

Sites not aligning to the query:

256:258 HKH→KKK: Does not affect cobalamin-binding.

3ezxA Structure of methanosarcina barkeri monomethylamine corrinoid protein
31% identity, 80% coverage: 10:178/211 of query aligns to 11:181/212 of 3ezxA

query
sites
3ezxA

N

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active site: D100 (= D99), H102 (= H101), S155 (≠ A152)
binding 5-hydroxybenzimidazolylcobamide: M47 (≠ T45), F54 (= F52), D100 (= D99), I101 (≠ V100), H102 (= H101), D103 (= D102), I104 (= I103), V109 (= V108), V147 (vs. gap), S149 (= S146), L151 (= L148), M152 (≠ L149), T153 (= T150), M178 (≠ V175), G180 (= G177), G181 (= G178)

Sites not aligning to the query:

binding 5-hydroxybenzimidazolylcobamide: 198, 200

Q99707 Methionine synthase; MS; 5-methyltetrahydrofolate--homocysteine methyltransferase; Cobalamin-dependent methionine synthase; Vitamin-B12 dependent methionine synthase; EC 2.1.1.13 from Homo sapiens (Human) (see 6 papers)
30% identity, 73% coverage: 24:178/211 of query aligns to 696:860/1265 of Q99707

query
sites
Q99707

L

L

N

N

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G

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K

N

N

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G

Sites not aligning to the query:

61 natural variant: R -> K
255 C → Y: in dbSNP:rs1140598
382:384 binding (6S)-5,6,7,8-tetrahydrofolate
449 binding (6S)-5,6,7,8-tetrahydrofolate
470 binding (6S)-5,6,7,8-tetrahydrofolate
537 binding (6S)-5,6,7,8-tetrahydrofolate
579 binding (6S)-5,6,7,8-tetrahydrofolate
585 binding (6S)-5,6,7,8-tetrahydrofolate
591 binding (6S)-5,6,7,8-tetrahydrofolate
919 D → G: in dbSNP:rs1805087
963 D→E: Decreases binding to MTRR; when associated with N-1071.
1071 K→N: Decreases binding to MTRR; when associated with E-963.

8j2xA Saccharothrix syringae photocobilins protein, light state (see paper)
26% identity, 82% coverage: 5:178/211 of query aligns to 8:176/337 of 8j2xA

query
sites
8j2xA

N

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K

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V

R

L

F
x
W

E
x
Q

E

A

G

N

R

R

Y

W

F

S

V

V

S

A

D

Q

L

E

M

H

M

A

A

A

G

T

E

A

I

I

L

S

S

E

Q

R

I

-

M

-

V

V

I

I

L

A

K

A

P

V

L

G

F

D

G

R

E

A

H

A

K

A

I

A

A

P

S

T

K

R

G

G

L

H

I

V

V

V

G

A

T

C

V

L

Q

D

G

G

D

E

V
x
W

H
|
H

D
x
A

I
x
L

G
x
P

K

A

N

R

I

I

V
|
V

A

A

A

E

L

V

L

L

E

R

A

G

E

R

G

G

F

W

D

R

V

V

V

T

D

F

I

L

G

G

V

A

D

S

Q

V

P

P

P

A

E

A

E

H

F

L

V

V

K

P

A

Y

I

L

R

E

E

E

H

H

H

G

P

P

K

D

V

A

V

V

S
x
A

L
|
L

S
|
S

G

C

L

T

L
|
L

T

P

E

R

A

G

I

L

E

P

S

R

M

A

K

D

T

Q

T

V

I

V

E

A

A

A

I

C

K

R

A

A

A

T

G

G

L

-

R

-

D

-

Q

-

V

T

K

P

I

V

V
x
L

I
x
V

G
|
G

binding cobalamin: A46 (≠ R42), Q49 (≠ T45), G53 (= G49), W56 (≠ F52), Q57 (≠ E53), W102 (≠ V100), H103 (= H101), A104 (≠ D102), L105 (≠ I103), P106 (≠ G104), V110 (= V108), A146 (≠ S144), L147 (= L145), S148 (= S146), L151 (= L149), L173 (≠ V175), V174 (≠ I176), G175 (= G177), G176 (= G178)
binding biliverdine ix alpha: W56 (≠ F52)

Sites not aligning to the query:

binding cobalamin: 195, 196, 197, 198, 287
binding biliverdine ix alpha: 250, 253, 254, 257, 258, 261, 264, 287, 292, 295, 297, 301

8jbtA B12-binding domain from chloracidobacterium thermophilum merr family protein, anaerobic light state
29% identity, 46% coverage: 90:187/211 of query aligns to 105:203/228 of 8jbtA

query
sites
8jbtA

L

L

I

A

V

L

V

C

G

G

T

C

V

P

Q

E

G
|
G

D
|
D

V
x
L

H
|
H

D

E

I
|
I

G
x
A

K

L

N

H

I

L

V
|
V

A

M

A

E

L

V

L

L

E

E

A

V

E

E

G

G

F

W

D

R

V

V

V

L

D

S

I

L

G

G

V

P

D

N

Q

T

P

P

P

L

E

F

E

S

F

F

V

A

K

D

A

A

I

V

R

R

E

R

H

F

H

S

P

P

K

Q

V

L

V

V

S

C

L

I

S
|
S

G

A

L

T

L

I

T

V

E

H

A

D

I

L

E

E

S

R

M

L

K

R

T

R

T

D

I

Y

E

G

A

D

I

F

K

Y

A

H

A

T

G

V

L

R

R

Q

D

H

Q

G

V

A

K

R

I

I

V

V

I

I

G
|
G

G

A

R

A

-

F

C

A

D

D

E

P

E

Q

A

V

R

R

E

E

binding cobalamin: G113 (= G98), D114 (= D99), L115 (≠ V100), H116 (= H101), I118 (= I103), A119 (≠ G104), V123 (= V108), S161 (= S146), G192 (= G177), G193 (= G178)

Sites not aligning to the query:

binding cobalamin: 61, 62, 65, 68, 69, 75, 78, 82, 212, 217

1id8A Nmr structure of glutamate mutase (b12-binding subunit) complexed with the vitamin b12 nucleotide (see paper)
32% identity, 43% coverage: 88:178/211 of query aligns to 3:92/137 of 1id8A

query
sites
1id8A

K

K

G

K

L

T

I

I

V

V

V

L

G

G

T
x
V

V

I

Q

G

G

S

D
|
D

V

C

H
|
H

D

A

I

V

G

G

K

N

N

K

I

I

V

L

A

D

A

H

L

S

L

F

E

T

A

N

E

A

G

G

F

F

D

N

V

V

D

N

I

I

G

G

V

V

D

L

Q

S

P

S

P

Q

E

E

E

D

F

F

V

I

K

N

A

A

I

A

R

I

E

E

H

T

H

K

P

A

K

D

V

L

V

I

S

C

L

V

S
|
S

G

S

L
|
L

L

Y

T

G

E

Q

A

G

I

E

E

I

S

D

M

C

K

K

T

G

T

L

I

R

E

E

A

K

I

C

K

D

A

E

A

A

G

G

L

L

R

K

D

G

Q

-

V

I

K

K

I

L

V

F

I

V

G
|
G

G

G

active site: V10 (≠ T95), D14 (= D99), H16 (= H101)
binding phosphoric acid mono-[5-(5,6-dimethyl-benzoimidazol-1-yl)-4-hydroxy-2-hydroxymethyl-tetrahydro-furan-3-yl] ester: S61 (= S146), L63 (= L148), G91 (= G177)

Sites not aligning to the query:

binding phosphoric acid mono-[5-(5,6-dimethyl-benzoimidazol-1-yl)-4-hydroxy-2-hydroxymethyl-tetrahydro-furan-3-yl] ester: 117, 119, 121

1i9cA Glutamate mutase from clostridium cochlearium: complex with adenosylcobalamin and substrate (see paper)
32% identity, 43% coverage: 88:178/211 of query aligns to 3:92/137 of 1i9cA

query
sites
1i9cA

K

K

G

K

L

T

I

I

V

V

V

L

G

G

T
x
V

V

I

Q

G

G
x
S

D
|
D

V
x
C

H
|
H

D
x
A

I

V

G
|
G

K

N

N

K

I

I

V
x
L

A

D

A

H

L

A

L

F

E

T

A

N

E

A

G

G

F

F

D

N

V

V

D

N

I

I

G

G

V

V

D

L

Q

S

P

P

P

Q

E

E

E

N

F

F

V

I

K

K

A

A

I

A

R

I

E

E

H

T

H

K

P

A

K

D

V

A

V

I

S

L

L

V

S
|
S

G

S

L
|
L

L
x
Y

T
x
G

E

Q

A

G

I

E

E

I

S

D

M

C

K

K

T

G

T

L

I

R

E

Q

A

K

I

C

K

D

A

E

A

A

G

G

L

L

R

-

D

E

Q

G

V

I

K

L

I

L

V

Y

I

V

G
|
G

active site: V10 (≠ T95), D14 (= D99), H16 (= H101)
binding cobalamin: S13 (≠ G98), D14 (= D99), C15 (≠ V100), H16 (= H101), A17 (≠ D102), G19 (= G104), L23 (≠ V108), S61 (= S146), L63 (= L148), Y64 (≠ L149), G65 (≠ T150), G91 (= G177), G92 (= G178)

Sites not aligning to the query:

binding cobalamin: 93, 95, 96, 121

1ccwA Structure of the coenzyme b12 dependent enzyme glutamate mutase from clostridium cochlearium (see paper)
32% identity, 43% coverage: 88:178/211 of query aligns to 3:92/137 of 1ccwA

query
sites
1ccwA

K

K

G

K

L

T

I

I

V

V

V

L

G

G

T
x
V

V

I

Q

G

G

S

D
|
D

V
x
C

H
|
H

D
x
A

I

V

G
|
G

K

N

N

K

I
|
I

V

L

A

D

A

H

L

A

L

F

E

T

A

N

E

A

G

G

F

F

D

N

V

V

D

N

I

I

G

G

V

V

D

L

Q

S

P

P

P

Q

E

E

E

L

F

F

V

I

K

K

A

A

I

A

R

I

E

E

H

T

H

K

P

A

K

D

V

A

V

I

S

L

L

V

S
|
S

G

S

L
|
L

L
x
Y

T
x
G

E

Q

A

G

I

E

E

I

S

D

M

C

K

K

T

G

T

L

I

R

E

Q

A

K

I

C

K

D

A

E

A

A

G

G

L

L

R

-

D

E

Q

G

V

I

K

L

I

L

V

Y

I

V

G
|
G

active site: V10 (≠ T95), D14 (= D99), H16 (= H101)
binding cyanocobalamin: D14 (= D99), C15 (≠ V100), H16 (= H101), A17 (≠ D102), G19 (= G104), I22 (= I107), S61 (= S146), L63 (= L148), Y64 (≠ L149), G65 (≠ T150), G91 (= G177), G92 (= G178)

Sites not aligning to the query:

binding cyanocobalamin: 93, 95, 117, 121, 123

1cb7A Glutamate mutase from clostridium cochlearium reconstituted with methyl-cobalamin (see paper)
32% identity, 43% coverage: 88:178/211 of query aligns to 3:92/137 of 1cb7A

query
sites
1cb7A

K

K

G

K

L

T

I

I

V

V

V

L

G

G

T
x
V

V

I

Q

G

G

S

D
|
D

V
x
C

H
|
H

D
x
A

I

V

G
|
G

K

N

N

K

I

I

V
x
L

A

D

A

H

L

A

L

F

E

T

A

N

E

A

G

G

F

F

D

N

V

V

D

N

I

I

G

G

V

V

D

L

Q

S

P

P

P

Q

E

E

E

L

F

F

V

I

K

K

A

A

I

A

R

I

E

E

H

T

H

K

P

A

K

D

V

A

V

I

S

L

L

V

S
|
S

G

S

L
|
L

L
x
Y

T
x
G

E

Q

A

G

I

E

E

I

S

D

M

C

K

K

T

G

T

L

I

R

E

Q

A

K

I

C

K

D

A

E

A

A

G

G

L

L

R

-

D

E

Q

G

V

I

K

L

I

L

V

Y

I

V

G
|
G

active site: V10 (≠ T95), D14 (= D99), H16 (= H101)
binding co-methylcobalamin: D14 (= D99), C15 (≠ V100), H16 (= H101), A17 (≠ D102), G19 (= G104), L23 (≠ V108), S61 (= S146), L63 (= L148), Y64 (≠ L149), G65 (≠ T150), G91 (= G177), G92 (= G178)

Sites not aligning to the query:

binding co-methylcobalamin: 93, 95, 96, 121

E3PRJ4 Lysine 5,6-aminomutase beta subunit; 5,6-LAM; D-lysine 5,6-aminomutase beta subunit; L-beta-lysine 5,6-aminomutase beta subunit; EC 5.4.3.3 from Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF) (Clostridium sticklandii) (see paper)
27% identity, 54% coverage: 88:200/211 of query aligns to 119:250/262 of E3PRJ4

query
sites
E3PRJ4

K

R

G

K

L

I

I

V

V

V

G

G

T

A

V

S

Q

T

G

G

-
x
T

D
|
D

V
x
A

H
|
H

D
x
T

I
x
V

G
|
G

K

-

N

-

I

-

V

I

A

D

A

A

L

I

L

M

E

N

A

M

E
x
K

G

G

F

Y

-

A

-

G

-

H

-

Y

-

G

-

L

-

E

-

R

-

Y

-

E

-

M

-

I

D

D

V

A

V

Y

D

N

I

L

G

G

V

S

D

Q

Q

V

P

A

P

N

E

E

E

D

F

F

V

I

K

K

A

K

I

A

R

V

E

E

H

L

H

E

P

A

K

D

V

V

V

L

S
x
L

L
x
V

S
|
S

G
x
Q

L
x
T

L
x
V

T
|
T

E
x
Q

A

K

-

N

-

V

-

H

I

I

E

Q

S

N

M

M

K

T

T

H

T

L

I

I

E

E

A

L

I

L

K

E

A

A

A

E

G

G

L

L

R

R

D

D

Q

R

V

F

K

V

I

L

V
x
L

I
x
C

G
|
G

G
x
P

R

R

C

I

D

N

E

N

E

E

A

I

R

A

E

K

Y

E

T

L

T

G

A

Y

D

D

A

A

-

G

-
x
F

-
x
G

-
x
P

-
x
G

-
x
R

W
x
F

A

A

D

D

A

V

A

A

V

T

130:136 (vs. 99:104, 43% identical) binding adenosylcob(III)alamin
K144 (≠ E115) modified: N6-(pyridoxal phosphate)lysine
185:192 (vs. 144:151, 25% identical) binding adenosylcob(III)alamin
LCGGP 219:223 (≠ VIGGG 175:179) binding adenosylcob(III)alamin
FGPGRF 239:244 (≠ -----W 194) binding adenosylcob(III)alamin

Query Sequence

>WP_109967067.1 NCBI__GCF_003173355.1:WP_109967067.1
MTNLNEDFINALVDLDETTCIDLLNQRIAAKENPMNILEDVRKSTDIVGKRFEEGRYFVS
DLMMAGEILSQIMVILKPLFGEHKIASKGLIVVGTVQGDVHDIGKNIVAALLEAEGFDVV
DIGVDQPPEEFVKAIREHHPKVVSLSGLLTEAIESMKTTIEAIKAAGLRDQVKIVIGGGR
CDEEAREYTTADAWADDAAVGVRKIKELAGV

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory