SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing HSERO_RS16505 HSERO_RS16505 3-isopropylmalate dehydratase small subunit 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 14 hits to proteins with known functional sites (download)

O14289 3-isopropylmalate dehydratase; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
51% identity, 98% coverage: 3:212/215 of query aligns to 539:735/758 of O14289

query
sites
O14289

K

K

F

F

I

T

V

V

H

V

E

E

G

G

L

I

V

A

A

A

P

P

L

L

D

P

R

M

A

A

N

N

V

V

D

D

T

T

D

D

A

K

I

I

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P

K

K

Q

Q

F

F

L

L

K

K

S

T

I

I

K

K

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R

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T

G

G

F

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G

G

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Q

N

F

L

A

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F

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Y

E

E

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I

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R

Y

Y

L

D

D

A

H

D

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G

E

K

P

E

G

-

M

-

D

-

N

-

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D

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F

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E

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H

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P

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A

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P

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S

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F

A

A

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D

I

I

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F

N

N

C

C

Y

F

K

K

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N

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G

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M

L

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T

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E

I

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E

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D

L

M

F

M

N

K

E

-

V

-

K

A

A

A

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Y

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N

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N

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P

W

W

L

M

S

N

Sites not aligning to the query:

486 modified: Phosphoserine
488 modified: Phosphoserine

P9WK95 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
40% identity, 97% coverage: 1:209/215 of query aligns to 1:192/198 of P9WK95

query
sites
P9WK95

M

M

N

E

K

A

F

F

I

H

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T

H

H

E

S

G

G

L

I

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A

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P

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N

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A

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F

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L

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K

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K

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R

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T

G

G

F

F

G

E

P

D

N

G

L

L

F

F

D

A

E

G

W

W

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R

Y

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L

-

D

-

H

-

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E

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G

-

M

-

D

-

N

-

S

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K

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R

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P

-

L

-

N

D

P

P

D

A

F

F

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V

L

L

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N

Q

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E

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S

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D

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P

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E
x
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P

K154 (≠ E171) modified: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)

Q58667 Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
31% identity, 72% coverage: 18:171/215 of query aligns to 13:137/170 of Q58667

query
sites
Q58667

N

D

V

V

D

D

T

T

D

D

A

A

I

I

P

P

K

G

Q

P

F

Y

L

L

K
x
R

S
x
T

I

T

K

-

R

-

S

-

G

-

F

-

G

-

P

-

N

-

L

-

F

-

D

D

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Y

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Y

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L

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H

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A

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D

N

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K

-

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N

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D

-

F

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N

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Y

N

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A

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N

N

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G

L

L

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D

L

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E

-

V

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K

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A

-

F

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-

G

G

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D

L

L

E

D

K

K

Q

E

I

E

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S

V

T

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T

T

N

N

G

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S

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E

R26 (≠ K31) mutation R->K,V: Allows the recognition of substrates of IPMI enzymes since it becomes able to efficiently catalyze citraconate hydration and 3-isopropylmalate dehydration. Largely decreases substrate affinity for cis-homo(1-3)-aconitate.
T27 (≠ S32) mutation to A: Largely decreases substrate affinity for cis-homo(1-3)-aconitate while slightly increases activity on these substrates, and also decreases substrate affinity for maleate. Gains the ability to hydrate citraconate, an IPMI substrate.

2pkpA Crystal structure of 3-isopropylmalate dehydratase (leud)from methhanocaldococcus jannaschii dsm2661 (mj1271) (see paper)
31% identity, 72% coverage: 18:171/215 of query aligns to 13:137/167 of 2pkpA

query
sites
2pkpA

N
x
D

V

V

D

D

T

T

D

D

A

A

I

I

P

P

K

G

Q

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F

Y

L

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K

R

S

T

I

T

K

-

R

-

S

-

G

-

F

-

G

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P

-

N

-

L

-

F

-

D

D

E

P

W

Y

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E

Y

L

L

A

D

S

H

H

G

C

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M

P

A

G

G

M

I

D

D

N

E

S

N

K

-

R

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P

-

L

-

N

-

P

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D

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E

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E

N

N

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C
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C

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A

A

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F

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F

F

Y

N

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N

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A

Y

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N

N

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G

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L

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F

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N

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E

binding zinc ion: D13 (≠ N18), C63 (= C88)

P20004 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Bos taurus (Bovine) (see 2 papers)
37% identity, 32% coverage: 65:132/215 of query aligns to 644:711/780 of P20004

query
sites
P20004

P

P

D

D

F

T

V

A

L

R

N

Y

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Y

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G

G

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V

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E

N

N

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Y

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E

G

G

S

S

S
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R

E

E

H

H

A

A

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A

W

L

A

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H

F

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G

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I

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F

E

N

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N

N

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N

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G

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P

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D

SR 670:671 (= SR 91:92) binding

Sites not aligning to the query:

99 binding
192:194 binding
385 binding
448 binding
451 binding
474 binding
479 binding
607 binding

5acnA Structure of activated aconitase. Formation of the (4fe-4s) cluster in the crystal (see paper)
36% identity, 41% coverage: 79:166/215 of query aligns to 631:722/754 of 5acnA

query
sites
5acnA

I

V

L

V

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E

N

N

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C

E

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R

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E

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A

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H

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R

A

A

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I

A

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K

S

S

F

F

A

A

D
x
R

I

I

F

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F

E

N

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N

N

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K

K

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G

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A

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Y

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D

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L

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G

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K

A

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F

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A

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N

N

G

G

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T

Q

Q

active site: S642 (= S90), R644 (= R92)
binding tricarballylic acid: R666 (≠ D114)

Sites not aligning to the query:

active site: 100, 101, 165, 447
binding fe3-s4 cluster: 145, 147, 167, 358, 421, 424, 446
binding tricarballylic acid: 198, 235

1b0kA S642a:fluorocitrate complex of aconitase (see paper)
35% identity, 41% coverage: 79:166/215 of query aligns to 630:721/753 of 1b0kA

query
sites
1b0kA

I

V

L

V

L

I

S

G

R

D

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E

N

N

F

Y

G

G

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x
A

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R

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E

H

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K

A

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F

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A

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-

I

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D

-

L

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-

K

K

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T

P

N

N

G

G

S

T

Q

Q

active site: A641 (≠ S90), R643 (= R92)
binding citrate anion: A641 (≠ S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding citrate anion: 71, 100, 164, 165, 446, 451, 579
binding oxygen atom: 164, 166
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423

P16276 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Sus scrofa (Pig) (see 3 papers)
36% identity, 41% coverage: 79:166/215 of query aligns to 658:749/781 of P16276

query
sites
P16276

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S

S

S
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S

R
|
R

E

E

H

H

A

R

P

A

W

L

A

E

L

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H

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L

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R

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I

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P

K

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S

F

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N

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K

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G

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P

I

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L

F

T

A

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D

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A

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Y

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D

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L

L

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G

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K

K

A

D

F

F

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A

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P

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I

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D

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L

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E

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K

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C

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K

T

H

T

P

N

N

G

G

S

T

Q

Q

SR 670:671 (= SR 91:92) binding

Sites not aligning to the query:

28 modified: Pyrrolidone carboxylic acid
99 binding
192:194 binding
385 binding
448 binding
451 binding
474 binding
479 binding
607 binding

8acnA Crystal structures of aconitase with isocitrate and nitroisocitrate bound (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 8acnA

query
sites
8acnA

I

V

L

V

L

I

S

G

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D

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E

N

N

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Y

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R

E

E

H

H

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A

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L

A

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F

F

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I

I

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S

F

F

A

A

D

R

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I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding nitroisocitric acid: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding nitroisocitric acid: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423, 424

1fghA Complex with 4-hydroxy-trans-aconitate (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1fghA

query
sites
1fghA

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

D

R

Q

F

F

L

G

G

F

G

R

R

A

A

V

I

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding 4-hydroxy-aconitate ion: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding 4-hydroxy-aconitate ion: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423, 424, 451

1amjA Steric and conformational features of the aconitase mechanism (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1amjA

query
sites
1amjA

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

S

S

R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

D

R

Q

F

F

L

G

G

F

G

R

R

A

A

V

I

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding sulfate ion: R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding iron/sulfur cluster: 144, 166, 357, 420, 423
binding sulfate ion: 71, 579

1amiA Steric and conformational features of the aconitase mechanism (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1amiA

query
sites
1amiA

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

D

R

Q

F

F

L

G

G

F

G

R

R

A

A

V

I

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding alpha-methylisocitric acid: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding alpha-methylisocitric acid: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 144, 164, 166, 356, 357, 420, 423, 445

1acoA Crystal structure of aconitase with transaconitate bound (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1acoA

query
sites
1acoA

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

D

R

Q

F

F

L

G

G

F

G

R

R

A

A

V

I

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding aconitate ion: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding iron/sulfur cluster: 100, 144, 164, 166, 356, 357, 420, 423, 445
binding aconitate ion: 71, 164, 165, 446, 451, 579

1nisA Crystal structure of aconitase with trans-aconitate and nitrocitrate bound (see paper)
41% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1nisA

query
sites
1nisA

I

V

L

V

L

I

S

G

R

D

K

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

R

P

A

W

L

A

E

L

P

D

R

Q

F

F

L

G

G

F

G

R

R

A

A

V

I

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

F

E

N

T

N

N

C

L

Y

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

T

A

E

D

active site: S641 (= S90), R643 (= R92)
binding 2-hydroxy-2-nitromethyl succinic acid: S641 (= S90), S642 (= S91)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding 2-hydroxy-2-nitromethyl succinic acid: 71, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 144, 166, 356, 357, 420, 423

Query Sequence

>HSERO_RS16505 HSERO_RS16505 3-isopropylmalate dehydratase small subunit
MNKFIVHEGLVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDHGEPGMDNSK
RPLNPDFVLNQERYQGSSILLSRKNFGCGSSREHAPWALDQFGFRAVIAPSFADIFFNNC
YKNGLLPIVLTEQQVDHLFNEVKAFPGYRLVIDLEKQIVSTTNGSQTYPFEISEFRKYCL
LNGFDDIGLTLRKADTIRAYEEKHLHEQPWLSNTI

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