COLD_YERPU
ID COLD_YERPU Reviewed; 393 AA.
AC G4WJD4;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 14-DEC-2011, sequence version 1.
DT 03-AUG-2022, entry version 32.
DE RecName: Full=GDP-4-keto-6-deoxy-D-mannose 3-dehydratase {ECO:0000303|PubMed:15610039};
DE EC=4.2.1.168 {ECO:0000269|PubMed:15610039};
GN Name=colD {ECO:0000303|PubMed:15610039}; Synonyms=colA;
OS Yersinia pseudotuberculosis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=633 {ECO:0000312|EMBL:AEP25496.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=H720/86;
RX PubMed=21325338; DOI=10.1093/glycob/cwr010;
RA Cunneen M.M., Pacinelli E., Song W.C., Reeves P.R.;
RT "Genetic analysis of the O-antigen gene clusters of Yersinia
RT pseudotuberculosis O:6 and O:7.";
RL Glycobiology 21:1140-1146(2011).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP PATHWAY, AND SUBUNIT.
RX PubMed=15610039; DOI=10.1021/bi0483763;
RA Alam J., Beyer N., Liu H.W.;
RT "Biosynthesis of colitose: expression, purification, and mechanistic
RT characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and
RT GDP-L-colitose synthase (ColC).";
RL Biochemistry 43:16450-16460(2004).
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. {ECO:0000269|PubMed:15610039}.
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:15610039};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:15610039};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=8.5 uM for GDP-4-keto-6-deoxy-D-mannose (at pH 7 and 37 degrees
CC Celsius) {ECO:0000269|PubMed:15610039};
CC KM=1.4 mM for L-glutamate (at pH 7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15610039};
CC Note=kcat is 0.6 sec(-1) (at pH 7 and 37 degrees Celsius).
CC {ECO:0000269|PubMed:15610039};
CC -!- PATHWAY: Nucleotide-sugar metabolism; GDP-L-colitose biosynthesis.
CC {ECO:0000305|PubMed:15610039}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15610039}.
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; HQ456392; AEP25496.1; -; Genomic_DNA.
DR AlphaFoldDB; G4WJD4; -.
DR SMR; G4WJD4; -.
DR KEGG; ag:AEP25496; -.
DR BRENDA; 4.2.1.168; 4560.
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:0016595; F:glutamate binding; IDA:UniProtKB.
DR GO; GO:0016836; F:hydro-lyase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0009225; P:nucleotide-sugar metabolic process; IDA:UniProtKB.
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 Cell membrane; Lyase; Membrane; Pyridoxal phosphate; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..393
FT /note="GDP-4-keto-6-deoxy-D-mannose 3-dehydratase"
FT /id="PRO_0000435690"
FT TRANSMEM 53..73
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ACT_SITE 192
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:D3QY10"
FT BINDING 30..33
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:0000250|UniProtKB:D3QY10"
FT BINDING 60..61
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:0000250|UniProtKB:D3QY10"
FT BINDING 92
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:0000250|UniProtKB:D3QY10"
FT BINDING 166
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:0000250|UniProtKB:D3QY10"
FT BINDING 187
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:0000250|UniProtKB:D3QY10"
FT BINDING 219
FT /ligand="L-glutamate"
FT /ligand_id="ChEBI:CHEBI:29985"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:D3QY10"
FT BINDING 223
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:0000250|UniProtKB:D3QY10"
FT BINDING 252
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:D3QY10"
FT BINDING 254
FT /ligand="L-glutamate"
FT /ligand_id="ChEBI:CHEBI:29985"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:D3QY10"
FT BINDING 333
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:0000250|UniProtKB:D3QY10"
SQ SEQUENCE 393 AA; 44549 MW; 92AF59FFAAC7CA5D CRC64;
MRKIMINFPL ASSTWDEKEL NAIQRIIDSN MFTMGESVKQ YEKDFAEYFG SKYSVMVSSG
STANLLMIAA LFFTKKPKFK RGDEVIVPAV SWSTTYFPLQ QYGLNVRFVD IDKKTLNIDL
DKLKSAITEK TKAILAVNLL GNPNDFDAIT KITEGKDIFI LEDNCESMGA RLNGKQAGTY
GLMGTFSSFF SHHIATMEGG CVITDDEELY HILLCIRAHG WTRNLPEFNH ITGQKSIDPF
EESFKFVLPG YNVRPLEMSG AIGIEQLKKL PSFIEMRRKN ATIFKELFSS HPYIDIQQET
GESSWFGFAL ILKESSPITR AELVKKLIEA GIECRPIVTG NFLKNKEVLK FFDYTIAGEV
TDAEYIDKHG LFVGNHQIDL SEQIKNLFNI LKK
