SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing GFF2932 PGA1_c29790 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 8 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)
59% identity, 100% coverage: 1:201/201 of query aligns to 537:734/758 of O14289

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O14289

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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)
41% identity, 99% coverage: 1:199/201 of query aligns to 1:192/198 of P9WK95

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K154 (≠ E161) 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)
32% identity, 72% coverage: 18:161/201 of query aligns to 13:137/170 of Q58667

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Q58667

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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)
32% identity, 72% coverage: 18:161/201 of query aligns to 13:137/167 of 2pkpA

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binding zinc ion: D13 (≠ N18), C63 (= C79)

P20004 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Bos taurus (Bovine) (see 2 papers)
42% identity, 26% coverage: 70:121/201 of query aligns to 658:709/780 of P20004

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P20004

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SR 670:671 (= SR 82:83) 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)
40% identity, 26% coverage: 70:121/201 of query aligns to 631:682/754 of 5acnA

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active site: S642 (= S81), R644 (= R83)
binding tricarballylic acid: R666 (≠ D105)

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

P19414 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
37% identity, 32% coverage: 65:129/201 of query aligns to 647:724/778 of P19414

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P19414

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Sites not aligning to the query:

1:16 modified: transit peptide, Mitochondrion
604 R→K: Strongly diminishes the catalytic activity towards both known substrates, aconitate and homoaconitate.

P39533 Homocitrate dehydratase, mitochondrial; Aconitase 2; EC 4.2.1.- from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
26% identity, 65% coverage: 48:177/201 of query aligns to 636:785/789 of P39533

query
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P39533

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Sites not aligning to the query:

610 K→R: Reduces catalytic activity towards homoaconitate by 45% and increases the activity towards aconitate by a factor 116.

Query Sequence

>GFF2932 PGA1_c29790 3-isopropylmalate dehydratase small subunit
MEKFTKIQGIAAPMPLVNIDTDMIIPKVFLKSIQRTGFGKNLFDEMRYNRDGSEIADFVL
NKPQYRDAEILIAGDNFGCGSSREHAPWAIADFGIRCIVSTSFADIFFNNSFKNGILPIV
LPQEQVDLLMKDAEKGANARMTVDLEAQEISTSDGEVIKFEVDAFKKHCLLNGLDDIGLT
MEKATSIASFEDKAAQERPWV

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