COLD_ECOCB
ID COLD_ECOCB Reviewed; 388 AA.
AC D3QY10;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 20-APR-2010, sequence version 1.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=GDP-4-keto-6-deoxy-D-mannose 3-dehydratase {ECO:0000303|PubMed:16943443};
DE EC=4.2.1.168 {ECO:0000269|PubMed:17997582, ECO:0000269|PubMed:18045869};
GN Name=colD {ECO:0000303|PubMed:16943443};
GN Synonyms=wbdK {ECO:0000312|EMBL:ADD57102.1};
GN OrderedLocusNames=G2583_2551 {ECO:0000312|EMBL:ADD57102.1};
OS Escherichia coli O55:H7 (strain CB9615 / EPEC).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=701177;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CB9615 / EPEC;
RX PubMed=20090843; DOI=10.1371/journal.pone.0008700;
RA Zhou Z., Li X., Liu B., Beutin L., Xu J., Ren Y., Feng L., Lan R.,
RA Reeves P.R., Wang L.;
RT "Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.";
RL PLoS ONE 5:E8700-E8700(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEXES WITH HYDRATED FORM OF
RP PLP AND A PLP-GLUTAMATE KETIMINE INTERMEDIATE, SUBUNIT, REACTION MECHANISM,
RP AND ACTIVE SITE.
RC STRAIN=5a;
RX PubMed=16943443; DOI=10.1110/ps.062328306;
RA Cook P.D., Thoden J.B., Holden H.M.;
RT "The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique
RT coenzyme B6-dependent enzyme.";
RL Protein Sci. 15:2093-2106(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF MUTANT LYS-188 IN COMPLEX WITH A
RP PLP-GLUTAMATE GEMINAL DIAMINE INTERMEDIATE, CATALYTIC ACTIVITY, AND
RP MUTAGENESIS OF HIS-188.
RC STRAIN=5a;
RX PubMed=17997582; DOI=10.1021/bi701686s;
RA Cook P.D., Holden H.M.;
RT "A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught
RT in the act of geminal diamine formation.";
RL Biochemistry 46:14215-14224(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT ASN-188 IN COMPLEX WITH
RP GDP-PEROSAMINE COVALENTLY LINKED TO PLP (EXTERNAL ALDIMINE), FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, PATHWAY, MUTAGENESIS
RP OF HIS-188, REACTION MECHANISM, AND ACTIVE SITE.
RC STRAIN=5a;
RX PubMed=18045869; DOI=10.1074/jbc.m708893200;
RA Cook P.D., Holden H.M.;
RT "GDP-4-keto-6-deoxy-D-mannose 3-dehydratase, accommodating a sugar
RT substrate in the active site.";
RL J. Biol. Chem. 283:4295-4303(2008).
CC -!- FUNCTION: Involved in the biosynthesis of L-colitose, a 3,6-
CC dideoxyhexose present in the O-antigen region of lipopolysaccharides
CC (LPS), where it serves as an antigenic determinant and is vital for
CC bacterial defense and survival. Catalyzes the removal of the C3'-
CC hydroxyl group from GDP-4-keto-6-deoxy-D-mannose via a combined
CC transamination-deoxygenation reaction. The catalysis is initiated by a
CC transamination step in which pyridoxal 5'-phosphate (PLP) is converted
CC to pyridoxamine 5'-phosphate (PMP) in the presence of L-glutamate. This
CC coenzyme then forms a Schiff base with GDP-4-keto-6-deoxy-D-mannose and
CC the resulting adduct undergoes a PMP-mediated beta-dehydration reaction
CC to give a sugar enamine intermediate, which after tautomerization and
CC hydrolysis to release ammonia yields GDP-4-keto-3,6-dideoxy-D-mannose
CC as a product. In vitro, is able to catalyze the formation of GDP-4-
CC keto-3,6-dideoxymannose using GDP-perosamine rather than GDP-4-keto-6-
CC deoxymannose as a substrate, with no need of glutamate.
CC {ECO:0000269|PubMed:18045869}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = 2-oxoglutarate
CC + GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + NH4(+);
CC Xref=Rhea:RHEA:49488, ChEBI:CHEBI:16810, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:57964, ChEBI:CHEBI:73931;
CC EC=4.2.1.168; Evidence={ECO:0000269|PubMed:17997582,
CC ECO:0000269|PubMed:18045869};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:18045869};
CC -!- PATHWAY: Nucleotide-sugar metabolism; GDP-L-colitose biosynthesis.
CC {ECO:0000305|PubMed:18045869}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16943443}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255}; Single-pass membrane
CC protein {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the DegT/DnrJ/EryC1 family. {ECO:0000305}.
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DR EMBL; CP001846; ADD57102.1; -; Genomic_DNA.
DR RefSeq; WP_000611604.1; NC_013941.1.
DR PDB; 2GMS; X-ray; 1.80 A; A/B=1-388.
DR PDB; 2GMU; X-ray; 1.90 A; A/B=1-388.
DR PDB; 2R0T; X-ray; 1.90 A; A/B=1-388.
DR PDB; 3B8X; X-ray; 1.70 A; A/B=1-388.
DR PDBsum; 2GMS; -.
DR PDBsum; 2GMU; -.
DR PDBsum; 2R0T; -.
DR PDBsum; 3B8X; -.
DR AlphaFoldDB; D3QY10; -.
DR SMR; D3QY10; -.
DR EnsemblBacteria; ADD57102; ADD57102; G2583_2551.
DR KEGG; eok:G2583_2551; -.
DR HOGENOM; CLU_033332_5_0_6; -.
DR OMA; FGVMGTF; -.
DR UniPathway; UPA01070; -.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR CDD; cd00616; AHBA_syn; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000653; DegT/StrS_aminotransferase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR30244; PTHR30244; 1.
DR Pfam; PF01041; DegT_DnrJ_EryC1; 1.
DR PIRSF; PIRSF000390; PLP_StrS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Lyase; Membrane; Pyridoxal phosphate;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..388
FT /note="GDP-4-keto-6-deoxy-D-mannose 3-dehydratase"
FT /id="PRO_0000439279"
FT TRANSMEM 49..69
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ACT_SITE 188
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:16943443,
FT ECO:0000305|PubMed:18045869"
FT BINDING 26..29
FT /ligand="GDP-4-dehydro-alpha-D-rhamnose"
FT /ligand_id="ChEBI:CHEBI:57964"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:3B8X"
FT BINDING 56..57
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:16943443,
FT ECO:0000305|PubMed:17997582, ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:2GMS"
FT BINDING 88
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:16943443,
FT ECO:0000305|PubMed:18045869, ECO:0007744|PDB:2GMS"
FT BINDING 162
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:16943443,
FT ECO:0000305|PubMed:18045869, ECO:0007744|PDB:2GMS"
FT BINDING 183
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:16943443,
FT ECO:0000305|PubMed:17997582, ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:2GMS"
FT BINDING 215
FT /ligand="L-glutamate"
FT /ligand_id="ChEBI:CHEBI:29985"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000305|PubMed:16943443,
FT ECO:0000305|PubMed:17997582, ECO:0007744|PDB:2GMU"
FT BINDING 219
FT /ligand="GDP-4-dehydro-alpha-D-rhamnose"
FT /ligand_id="ChEBI:CHEBI:57964"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:3B8X"
FT BINDING 248
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:16943443,
FT ECO:0000305|PubMed:17997582, ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:2GMS"
FT BINDING 250
FT /ligand="L-glutamate"
FT /ligand_id="ChEBI:CHEBI:29985"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000305|PubMed:16943443,
FT ECO:0000305|PubMed:17997582, ECO:0007744|PDB:2GMU"
FT BINDING 329
FT /ligand="GDP-4-dehydro-alpha-D-rhamnose"
FT /ligand_id="ChEBI:CHEBI:57964"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000305|PubMed:18045869,
FT ECO:0007744|PDB:3B8X"
FT MUTAGEN 188
FT /note="H->K,N: Loss of GDP-sugar dehydration activity."
FT /evidence="ECO:0000269|PubMed:17997582,
FT ECO:0000269|PubMed:18045869"
SQ SEQUENCE 388 AA; 44107 MW; 6E76DAF1513758B5 CRC64;
MINYPLASST WDDLEYKAIQ SVLDSKMFTM GEYVKQYETQ FAKTFGSKYA VMVSSGSTAN
LLMIAALFFT KKPRLKKGDE IIVPAVSWST TYYPLQQYGL RVKFVDIDIN TLNIDIESLK
EAVTDSTKAI LTVNLLGNPN NFDEINKIIG GRDIILLEDN CESMGATFNN KCAGTFGLMG
TFSSFYSHHI ATMEGGCIVT DDEEIYHILL CIRAHGWTRN LPKKNKVTGV KSDDQFEESF
KFVLPGYNVR PLEMSGAIGI EQLKKLPRFI SVRRKNAEYF LDKFKDHPYL DVQQETGESS
WFGFSFIIKK DSGVIRKQLV ENLNSAGIEC RPIVTGNFLK NTDVLKYFDY TVHNNVDNAE
YLDKNGLFVG NHQIELFDEI DYLREVLK
