ILVD_SYNY3
ID ILVD_SYNY3 Reviewed; 561 AA.
AC P74689;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Dihydroxy-acid dehydratase {ECO:0000255|HAMAP-Rule:MF_00012};
DE Short=DAD {ECO:0000255|HAMAP-Rule:MF_00012};
DE EC=4.2.1.9 {ECO:0000255|HAMAP-Rule:MF_00012};
GN Name=ilvD {ECO:0000255|HAMAP-Rule:MF_00012}; OrderedLocusNames=slr0452;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
CC -!- FUNCTION: Functions in the biosynthesis of branched-chain amino acids.
CC Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate
CC (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-
CC 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-
CC dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate),
CC the penultimate precursor to L-isoleucine and L-valine, respectively.
CC {ECO:0000255|HAMAP-Rule:MF_00012}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate
CC + H2O; Xref=Rhea:RHEA:24809, ChEBI:CHEBI:11851, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:49072; EC=4.2.1.9; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00012};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24810;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-
CC oxopentanoate + H2O; Xref=Rhea:RHEA:27694, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:35146, ChEBI:CHEBI:49258; EC=4.2.1.9;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27695;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis
CC acid cofactor. {ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC isoleucine from 2-oxobutanoate: step 3/4. {ECO:0000255|HAMAP-
CC Rule:MF_00012}.
CC -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC pyruvate: step 3/4. {ECO:0000255|HAMAP-Rule:MF_00012}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00012}.
CC -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000255|HAMAP-
CC Rule:MF_00012}.
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DR EMBL; BA000022; BAA18807.1; -; Genomic_DNA.
DR PIR; S76895; S76895.
DR PDB; 6NTE; X-ray; 2.33 A; A/B=1-561.
DR PDBsum; 6NTE; -.
DR AlphaFoldDB; P74689; -.
DR SMR; P74689; -.
DR IntAct; P74689; 6.
DR STRING; 1148.1653897; -.
DR PaxDb; P74689; -.
DR EnsemblBacteria; BAA18807; BAA18807; BAA18807.
DR KEGG; syn:slr0452; -.
DR eggNOG; COG0129; Bacteria.
DR InParanoid; P74689; -.
DR OMA; TQGRNMA; -.
DR PhylomeDB; P74689; -.
DR UniPathway; UPA00047; UER00057.
DR UniPathway; UPA00049; UER00061.
DR Proteomes; UP000001425; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004160; F:dihydroxy-acid dehydratase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009082; P:branched-chain amino acid biosynthetic process; IBA:GO_Central.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009099; P:valine biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.50.30.80; -; 1.
DR HAMAP; MF_00012; IlvD; 1.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR004404; DihydroxyA_deHydtase.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR020558; DiOHA_6PGluconate_deHydtase_CS.
DR InterPro; IPR037237; IlvD/EDD_N.
DR Pfam; PF00920; ILVD_EDD; 1.
DR SUPFAM; SSF143975; SSF143975; 1.
DR TIGRFAMs; TIGR00110; ilvD; 1.
DR PROSITE; PS00886; ILVD_EDD_1; 1.
DR PROSITE; PS00887; ILVD_EDD_2; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Amino-acid biosynthesis;
KW Branched-chain amino acid biosynthesis; Iron; Iron-sulfur; Lyase;
KW Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..561
FT /note="Dihydroxy-acid dehydratase"
FT /id="PRO_0000103520"
FT ACT_SITE 473
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 50
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 82
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 123
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 124
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 125
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 195
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 447
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT MOD_RES 125
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT STRAND 37..42
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 53..67
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 81..83
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 93..111
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 125..127
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 128..137
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 194..196
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 200..210
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 226..245
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 249..252
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 255..267
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 273..285
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 291..300
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 308..310
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 311..313
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 315..320
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 323..333
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 349..352
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 353..355
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 374..377
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 379..382
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 391..395
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 403..413
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 414..422
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 431..434
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 439..443
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 450..457
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 461..463
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 465..472
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 480..486
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 488..490
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 493..496
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 502..506
FT /evidence="ECO:0007829|PDB:6NTE"
FT TURN 507..510
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 511..514
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 518..527
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 538..546
FT /evidence="ECO:0007829|PDB:6NTE"
FT HELIX 550..552
FT /evidence="ECO:0007829|PDB:6NTE"
FT STRAND 556..559
FT /evidence="ECO:0007829|PDB:6NTE"
SQ SEQUENCE 561 AA; 58646 MW; 10A36D9EC02EAF4C CRC64;
MSNNPRSQVI TQGTQRSPNR AMLRAVGFGD DDFTKPIVGI ANGYSTITPC NMGINDLALR
AEAGLRTAGA MPQLFGTITI SDGISMGTEG MKYSLVSREV IADSIETVCN GQRMDGVLAI
GGCDKNMPGA MIAMARLNIP SIFVYGGTIK PGHYAGEDLT VVSAFEAVGQ YSAGKIDEET
LYGIERNACP GAGSCGGMFT ANTMSSAFEA MGMSLPYSST MAAVDGEKAD STEESAKVLV
EAIKKQILPS QILTRKAFEN AIAVIMAVGG STNAVLHLLA IANTIGVPLS LDDFETIRHK
VPVLCDLKPS GKYVTTNLHA AGGIPQVMKI LLVNGILHGD ALTITGQTIA EVLADIPDQP
PAGQDVIHSW DDPVYQEGHL AVLKGNLATE GSVAKISGVK KPVITGPAKV FESEEDCLEA
ILAGKIQAGD VVVVRYEGPK GGPGMREMLA PTSAIIGAGL GDSVGLITDG RFSGGTYGLV
VGHVAPEAYV GGAIALVQEG DQITIDAGKR LLQLNISEEE LAQRRAQWTP PQPRYPRGIL
AKYAKLVSSS SLGAVTDIDL F
