EVAA_AMYOR
ID EVAA_AMYOR Reviewed; 471 AA.
AC O52793;
DT 23-MAY-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase {ECO:0000303|PubMed:11035791};
DE EC=4.2.1.159 {ECO:0000269|PubMed:11035791, ECO:0000269|PubMed:23473392};
DE AltName: Full=2,3-dehydratase {ECO:0000303|PubMed:23473392};
GN Name=evaA {ECO:0000303|PubMed:11035791};
GN Synonyms=Orf23 {ECO:0000303|PubMed:11035791};
OS Amycolatopsis orientalis (Nocardia orientalis).
OC Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
OC Amycolatopsis.
OX NCBI_TaxID=31958;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9545426; DOI=10.1016/s1074-5521(98)90060-6;
RA van Wageningen A., Kirkpatrick P., Williams D., Harris B., Kershaw J.,
RA Lennard N., Jones M., Jones S., Solenberg P.;
RT "Sequencing and analysis of genes involved in the biosynthesis of a
RT vancomycin group antibiotic.";
RL Chem. Biol. 5:155-162(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=11035791; DOI=10.1073/pnas.210395097;
RA Chen H., Thomas M.G., Hubbard B.K., Losey H.C., Walsh C.T., Burkart M.D.;
RT "Deoxysugars in glycopeptide antibiotics: enzymatic synthesis of TDP-L-
RT epivancosamine in chloroeremomycin biosynthesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:11942-11947(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF MUTANT ALA-381 IN COMPLEX WITH
RP SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, MUTAGENESIS OF GLU-139; GLU-190; ASP-353; ARG-381; GLU-404;
RP GLU-405 AND GLU-452, DISULFIDE BONDS, SUBUNIT, AND REACTION MECHANISM.
RX PubMed=23473392; DOI=10.1021/bi400176n;
RA Kubiak R.L., Thoden J.B., Holden H.M.;
RT "Structure of EvaA: a paradigm for sugar 2,3-dehydratases.";
RL Biochemistry 52:2078-2088(2013).
CC -!- FUNCTION: Involved in the biosynthesis of the 2,3,6-trideoxysugar L-
CC epivancosamine, the terminal sugar added to the aglycone scaffold of
CC chloroeremomycin, a member of the glycopeptide antibiotics vancomycin
CC family. Catalyzes the removal of the hydroxyl group at position C-2 of
CC the hexose ring of dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose, and
CC the oxidation of the hydroxyl group at position C-3 to form a carbonyl
CC functionality. The product of the reaction, dTDP-2,6-dideoxy-D-glycero-
CC hex-2-enos-4-ulose, is a highly unstable diketosugar, which
CC spontaneously forms dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose.
CC {ECO:0000269|PubMed:11035791, ECO:0000269|PubMed:23473392}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-3,4-didehydro-
CC 2,6-dideoxy-alpha-D-glucose + H2O; Xref=Rhea:RHEA:47972,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:57649, ChEBI:CHEBI:84540;
CC EC=4.2.1.159; Evidence={ECO:0000269|PubMed:11035791,
CC ECO:0000269|PubMed:23473392};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=56 uM for dTDP-glucose {ECO:0000269|PubMed:23473392};
CC Vmax=4 umol/min/mg enzyme for dTDP-glucose
CC {ECO:0000269|PubMed:23473392};
CC -!- PATHWAY: Antibiotic biosynthesis. {ECO:0000305|PubMed:11035791}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23473392}.
CC -!- MISCELLANEOUS: The mutant Ala-381 is used to improve the quality of the
CC crystals. {ECO:0000269|PubMed:23473392}.
CC -!- MISCELLANEOUS: Two binding sites (pockets A and B) for the dTDP-sugar
CC ligands have been identified in each subunit. It seems that pocket A
CC represents the active site and pocket B is a vestige of the gene
CC duplication event. {ECO:0000269|PubMed:23473392}.
CC -!- SIMILARITY: Belongs to the hexose 2,3-dehydratase family.
CC {ECO:0000305}.
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DR EMBL; AJ223998; CAA11763.1; -; Genomic_DNA.
DR PIR; T17472; T17472.
DR PDB; 4J7G; X-ray; 1.70 A; A/B=1-471.
DR PDB; 4J7H; X-ray; 1.69 A; A/B=1-471.
DR PDBsum; 4J7G; -.
DR PDBsum; 4J7H; -.
DR AlphaFoldDB; O52793; -.
DR SMR; O52793; -.
DR BioCyc; MetaCyc:MON-18438; -.
DR BRENDA; 4.2.1.159; 315.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 3.90.79.40; -; 3.
DR InterPro; IPR005212; EvaA-like.
DR InterPro; IPR038153; EvaA-like_sf.
DR Pfam; PF03559; Hexose_dehydrat; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Disulfide bond; Lyase.
FT CHAIN 1..471
FT /note="dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-
FT dehydratase"
FT /id="PRO_0000444212"
FT REGION 155..159
FT /note="dTDP-4-dehydro-6-deoxy-alpha-D-glucose 1; pocket A"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G"
FT REGION 367..369
FT /note="dTDP-4-dehydro-6-deoxy-alpha-D-glucose 2; pocket B"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT REGION 372..373
FT /note="dTDP-4-dehydro-6-deoxy-alpha-D-glucose 2; pocket B"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT REGION 405..408
FT /note="dTDP-4-dehydro-6-deoxy-alpha-D-glucose 1; pocket A"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT BINDING 67
FT /ligand="dTDP-4-dehydro-6-deoxy-alpha-D-glucose"
FT /ligand_id="ChEBI:CHEBI:57649"
FT /ligand_label="1"
FT /note="from pocket A"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT BINDING 193
FT /ligand="dTDP-4-dehydro-6-deoxy-alpha-D-glucose"
FT /ligand_id="ChEBI:CHEBI:57649"
FT /ligand_label="2"
FT /note="from pocket B"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT BINDING 238
FT /ligand="dTDP-4-dehydro-6-deoxy-alpha-D-glucose"
FT /ligand_id="ChEBI:CHEBI:57649"
FT /ligand_label="1"
FT /note="from pocket A"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G"
FT BINDING 288
FT /ligand="dTDP-4-dehydro-6-deoxy-alpha-D-glucose"
FT /ligand_id="ChEBI:CHEBI:57649"
FT /ligand_label="2"
FT /note="from pocket B"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT BINDING 351
FT /ligand="dTDP-4-dehydro-6-deoxy-alpha-D-glucose"
FT /ligand_id="ChEBI:CHEBI:57649"
FT /ligand_label="2"
FT /note="from pocket B"
FT /evidence="ECO:0000305|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT DISULFID 286
FT /note="Interchain"
FT /evidence="ECO:0000269|PubMed:23473392,
FT ECO:0007744|PDB:4J7G, ECO:0007744|PDB:4J7H"
FT MUTAGEN 139
FT /note="E->Q: Loss of dehydratase activity."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 190
FT /note="E->A,Q: Loss of dehydratase activity."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 353
FT /note="D->A: Same dehydratase activity compared to the wild
FT type."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 381
FT /note="R->A: The mutation has little effect on the overall
FT catalytic efficiency of the enzyme."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 404
FT /note="E->Q: Loss of dehydratase activity."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 405
FT /note="E->A,Q: Loss of dehydratase activity."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 452
FT /note="E->A: Loss of dehydratase activity."
FT /evidence="ECO:0000269|PubMed:23473392"
FT MUTAGEN 452
FT /note="E->Q: Same dehydratase activity compared to the wild
FT type."
FT /evidence="ECO:0000269|PubMed:23473392"
FT HELIX 21..29
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 38..51
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:4J7H"
FT TURN 71..73
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 85..94
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 104..112
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 129..138
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 156..158
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 182..189
FT /evidence="ECO:0007829|PDB:4J7H"
FT TURN 192..194
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 199..206
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 217..221
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 222..229
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 237..244
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 259..271
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 274..280
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 288..290
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 302..311
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 320..329
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 331..340
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 343..352
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 365..368
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 370..373
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 378..380
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 385..389
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 393..395
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 396..403
FT /evidence="ECO:0007829|PDB:4J7H"
FT TURN 406..408
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 409..411
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 413..420
FT /evidence="ECO:0007829|PDB:4J7H"
FT STRAND 431..434
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 436..442
FT /evidence="ECO:0007829|PDB:4J7H"
FT HELIX 451..465
FT /evidence="ECO:0007829|PDB:4J7H"
SQ SEQUENCE 471 AA; 53023 MW; 9D8ED63C2C98CA51 CRC64;
MSSFVVPSLT AVRPRDHHDY ADRIALSAAT TDGVQMRTED VRAWIAERRD ANVFHVERIP
FADLDQWWFE GVTGNLVHRS GRFFTIEGLH VIEHDGPHGD GPYREWQQPV IRQPEVGILG
ILAKEFDGVL HFLMQAKMEP GNPNLVQLSP TVQATRSNYT KAHGGTNVKL IEYFAPPDPE
RVIVDVLQAE QGSWFFRKSN RNMIVETVDD VPLWDDFCWL TLGQIAELMH EDETINMNSR
SVLSCLPYQD ITPRALFSDV QLLSWFTNER SRHDVRVRRI PLADVCGWKQ GAEEIEHEDG
RYFKVLAVAV KGSNREKISW TQPLVESVDL GVVAFLVRKI DGVPHVLVQA RVDGGFLDTV
ELAPTVQCTP LNYAHLPAEE RPPFLDLVQN APRSRIRYEA IHSEEGGRFL GVRARYLVID
ADEAIDPPPG YAWVTPAQLT ALTRHGHYVN VEARTLLACI NAAAAQPRGG A
