G4WJD4 · COLD_YERPU

  • Protein
    GDP-4-keto-6-deoxy-D-mannose 3-dehydratase
  • Gene
    colD
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

Involved in the biosynthesis of L-colitose, a 3,6-dideoxyhexose present in the O-antigen region of lipopolysaccharides (LPS), where it serves as an antigenic determinant and is vital for bacterial defense and survival. Catalyzes the removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxy-D-mannose via a combined transamination-deoxygenation reaction. The catalysis is initiated by a transamination step in which pyridoxal 5'-phosphate (PLP) is converted to pyridoxamine 5'-phosphate (PMP) in the presence of L-glutamate. This coenzyme then forms a Schiff base with GDP-4-keto-6-deoxy-D-mannose and the resulting adduct undergoes a PMP-mediated beta-dehydration reaction to give a sugar enamine intermediate, which after tautomerization and hydrolysis to release ammonia yields GDP-4-keto-3,6-dideoxy-D-mannose as a product.

Catalytic activity

Cofactor

pyridoxal 5'-phosphate (UniProtKB | Rhea| CHEBI:597326 )

Kinetics

KM SUBSTRATE pH TEMPERATURE[C] NOTES EVIDENCE
8.5 μMGDP-4-keto-6-deoxy-D-mannose737
1.4 mML-glutamate737
kcat is 0.6 sec-1 (at pH 7 and 37 degrees Celsius).

Pathway

Nucleotide-sugar metabolism; GDP-L-colitose biosynthesis.

Features

Showing features for binding site, active site.

TypeIDPosition(s)Description
Binding site30-33GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners
Binding site60-61pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain
Binding site92pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain
Binding site166pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain
Binding site187pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain
Active site192Proton donor/acceptor
Binding site219L-glutamate (UniProtKB | ChEBI); ligand shared between dimeric partners
Binding site223GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners
Binding site252pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners
Binding site254L-glutamate (UniProtKB | ChEBI); ligand shared between dimeric partners
Binding site333GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain

GO annotations

AspectTerm
Cellular Componentplasma membrane
Molecular Functionglutamate binding
Molecular Functionhydro-lyase activity
Molecular Functionprotein homodimerization activity
Molecular Functionpyridoxal phosphate binding
Molecular Functiontransaminase activity
Biological Processnucleotide-sugar metabolic process
Biological Processpolysaccharide biosynthetic process

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    GDP-4-keto-6-deoxy-D-mannose 3-dehydratase
  • EC number

Gene names

    • Name
      colD
    • Synonyms
      colA

Organism names

  • Taxonomic identifier
  • Strain
    • H720/86
  • Taxonomic lineage
    Bacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Yersiniaceae > Yersinia

Accessions

  • Primary accession
    G4WJD4

Subcellular Location

Cell membrane
; Single-pass membrane protein

Features

Showing features for transmembrane.

TypeIDPosition(s)Description
Transmembrane53-73Helical

Keywords

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00004356901-393GDP-4-keto-6-deoxy-D-mannose 3-dehydratase

Interaction

Subunit

Homodimer.

Structure

Family & Domains

Sequence similarities

Belongs to the DegT/DnrJ/EryC1 family.

Keywords

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    393
  • Mass (Da)
    44,549
  • Last updated
    2011-12-14 v1
  • Checksum
    92AF59FFAAC7CA5D
MRKIMINFPLASSTWDEKELNAIQRIIDSNMFTMGESVKQYEKDFAEYFGSKYSVMVSSGSTANLLMIAALFFTKKPKFKRGDEVIVPAVSWSTTYFPLQQYGLNVRFVDIDKKTLNIDLDKLKSAITEKTKAILAVNLLGNPNDFDAITKITEGKDIFILEDNCESMGARLNGKQAGTYGLMGTFSSFFSHHIATMEGGCVITDDEELYHILLCIRAHGWTRNLPEFNHITGQKSIDPFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPSFIEMRRKNATIFKELFSSHPYIDIQQETGESSWFGFALILKESSPITRAELVKKLIEAGIECRPIVTGNFLKNKEVLKFFDYTIAGEVTDAEYIDKHGLFVGNHQIDLSEQIKNLFNILKK

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
HQ456392
EMBL· GenBank· DDBJ
AEP25496.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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