SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing 7026625 Shewana3_3758 isopropylmalate isomerase small subunit (RefSeq) 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)
47% identity, 95% coverage: 4:194/201 of query aligns to 540:725/758 of O14289

query
sites
O14289

F

F

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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)
38% identity, 100% coverage: 1:200/201 of query aligns to 1:191/198 of P9WK95

query
sites
P9WK95

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K154 (≠ T163) 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)
35% identity, 71% coverage: 18:159/201 of query aligns to 13:143/170 of Q58667

query
sites
Q58667

N

D

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D

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R26 (≠ S31) 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 (= T34) 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)
35% identity, 71% coverage: 18:159/201 of query aligns to 13:143/167 of 2pkpA

query
sites
2pkpA

N
x
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binding zinc ion: D13 (≠ N18), C63 (= C81)

P20004 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Bos taurus (Bovine) (see 2 papers)
39% identity, 34% coverage: 56:124/201 of query aligns to 642:710/780 of P20004

query
sites
P20004

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SR 670:671 (= SR 84:85) 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)
38% identity, 34% coverage: 56:124/201 of query aligns to 615:683/754 of 5acnA

query
sites
5acnA

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A

active site: S642 (= S83), R644 (= R85)
binding tricarballylic acid: R666 (≠ D107)

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

P16276 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Sus scrofa (Pig) (see 3 papers)
38% identity, 34% coverage: 56:124/201 of query aligns to 642:710/781 of P16276

query
sites
P16276

P

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SR 670:671 (= SR 84:85) 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

1b0kA S642a:fluorocitrate complex of aconitase (see paper)
36% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1b0kA

query
sites
1b0kA

P

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A

active site: A641 (≠ S83), R643 (= R85)
binding citrate anion: A641 (≠ S83), S642 (= S84), R643 (= R85)

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

8acnA Crystal structures of aconitase with isocitrate and nitroisocitrate bound (see paper)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 8acnA

query
sites
8acnA

P

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A

active site: S641 (= S83), R643 (= R85)
binding nitroisocitric acid: S641 (= S83), S642 (= S84), R643 (= R85)

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)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1fghA

query
sites
1fghA

P

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A

active site: S641 (= S83), R643 (= R85)
binding 4-hydroxy-aconitate ion: S641 (= S83), S642 (= S84), R643 (= R85)

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)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1amjA

query
sites
1amjA

P

P

N

V

P

P

D

D

F

T

T

A

L

R

N

Y

K

Y

P

K

R

Q

Y

H

S

G

G

I

A

R

S

W

I

V

L

V

L

I

A

G

Q

D

E

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

A

R

D

F

F

L

G

G

L

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

G

T

N

N

S

L

I

K

N

K

N

Q

G

G

L

L

P

P

V

L

K

T

L

F

S

A

active site: S641 (= S83), R643 (= R85)
binding sulfate ion: R643 (= R85)

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)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1amiA

query
sites
1amiA

P

P

N

V

P

P

D

D

F

T

T

A

L

R

N

Y

K

Y

P

K

R

Q

Y

H

S

G

G

I

A

R

S

W

I

V

L

V

L

I

A

G

Q

D

E

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

A

R

D

F

F

L

G

G

L

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

G

T

N

N

S

L

I

K

N

K

N

Q

G

G

L

L

P

P

V

L

K

T

L

F

S

A

active site: S641 (= S83), R643 (= R85)
binding alpha-methylisocitric acid: S641 (= S83), S642 (= S84), R643 (= R85)

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)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1acoA

query
sites
1acoA

P

P

N

V

P

P

D

D

F

T

T

A

L

R

N

Y

K

Y

P

K

R

Q

Y

H

S

G

G

I

A

R

S

W

I

V

L

V

L

I

A

G

Q

D

E

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

A

R

D

F

F

L

G

G

L

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

G

T

N

N

S

L

I

K

N

K

N

Q

G

G

L

L

P

P

V

L

K

T

L

F

S

A

active site: S641 (= S83), R643 (= R85)
binding aconitate ion: S641 (= S83), S642 (= S84), R643 (= R85)

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)
38% identity, 34% coverage: 56:124/201 of query aligns to 614:682/753 of 1nisA

query
sites
1nisA

P

P

N

V

P

P

D

D

F

T

T

A

L

R

N

Y

K

Y

P

K

R

Q

Y

H

S

G

G

I

A

R

S

W

I

V

L

V

L

I

A

G

Q

D

E

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

A

R

D

F

F

L

G

G

L

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

G

T

N

N

S

L

I

K

N

K

N

Q

G

G

L

L

P

P

V

L

K

T

L

F

S

A

active site: S641 (= S83), R643 (= R85)
binding 2-hydroxy-2-nitromethyl succinic acid: S641 (= S83), S642 (= S84)

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

>7026625 Shewana3_3758 isopropylmalate isomerase small subunit (RefSeq)
MQPFTSHTGLAVMIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGEVPNPDF
TLNKPRYSGASILLAQENFGCGSSREHAPWALADFGLRAIIAPSFADIFYGNSINNGLLP
VKLSANEVRQLMDEVASEEGAQITVDLTTCKVTSPLGAEFSFTLAESARHKLLNGLDAIG
LTLSHGIQIGEYESQIPSWRC

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