G4WJD4 · COLD_YERPU
- ProteinGDP-4-keto-6-deoxy-D-mannose 3-dehydratase
- GenecolD
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids393 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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
- GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + 2-oxoglutarate + NH4+
Cofactor
Kinetics
KM | SUBSTRATE | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|---|
8.5 μM | GDP-4-keto-6-deoxy-D-mannose | 7 | 37 | |||
1.4 mM | L-glutamate | 7 | 37 |
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 30-33 | GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners | ||||
Sequence: NMFT | ||||||
Binding site | 60-61 | pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain | ||||
Sequence: GS | ||||||
Binding site | 92 | pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain | ||||
Sequence: W | ||||||
Binding site | 166 | pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain | ||||
Sequence: E | ||||||
Binding site | 187 | pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain | ||||
Sequence: S | ||||||
Active site | 192 | Proton donor/acceptor | ||||
Sequence: H | ||||||
Binding site | 219 | L-glutamate (UniProtKB | ChEBI); ligand shared between dimeric partners | ||||
Sequence: H | ||||||
Binding site | 223 | GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners | ||||
Sequence: R | ||||||
Binding site | 252 | pyridoxal 5'-phosphate (UniProtKB | ChEBI); ligand shared between dimeric partners | ||||
Sequence: N | ||||||
Binding site | 254 | L-glutamate (UniProtKB | ChEBI); ligand shared between dimeric partners | ||||
Sequence: R | ||||||
Binding site | 333 | GDP-4-dehydro-alpha-D-rhamnose (UniProtKB | ChEBI); ligand shared between dimeric partners; in other chain | ||||
Sequence: E |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | plasma membrane | |
Molecular Function | glutamate binding | |
Molecular Function | hydro-lyase activity | |
Molecular Function | protein homodimerization activity | |
Molecular Function | pyridoxal phosphate binding | |
Molecular Function | transaminase activity | |
Biological Process | nucleotide-sugar metabolic process | |
Biological Process | polysaccharide biosynthetic process |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameGDP-4-keto-6-deoxy-D-mannose 3-dehydratase
- EC number
Gene names
Organism names
- Organism
- Strain
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Yersiniaceae > Yersinia
Accessions
- Primary accessionG4WJD4
Subcellular Location
UniProt Annotation
GO Annotation
Cell membrane ; Single-pass membrane protein
Features
Showing features for transmembrane.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Transmembrane | 53-73 | Helical | ||||
Sequence: YSVMVSSGSTANLLMIAALFF |
Keywords
- Cellular component
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000435690 | 1-393 | GDP-4-keto-6-deoxy-D-mannose 3-dehydratase | |||
Sequence: MRKIMINFPLASSTWDEKELNAIQRIIDSNMFTMGESVKQYEKDFAEYFGSKYSVMVSSGSTANLLMIAALFFTKKPKFKRGDEVIVPAVSWSTTYFPLQQYGLNVRFVDIDKKTLNIDLDKLKSAITEKTKAILAVNLLGNPNDFDAITKITEGKDIFILEDNCESMGARLNGKQAGTYGLMGTFSSFFSHHIATMEGGCVITDDEELYHILLCIRAHGWTRNLPEFNHITGQKSIDPFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPSFIEMRRKNATIFKELFSSHPYIDIQQETGESSWFGFALILKESSPITRAELVKKLIEAGIECRPIVTGNFLKNKEVLKFFDYTIAGEVTDAEYIDKHGLFVGNHQIDLSEQIKNLFNILKK |
Interaction
Subunit
Homodimer.
Structure
Sequence
- Sequence statusComplete
- Length393
- Mass (Da)44,549
- Last updated2011-12-14 v1
- Checksum92AF59FFAAC7CA5D
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
HQ456392 EMBL· GenBank· DDBJ | AEP25496.1 EMBL· GenBank· DDBJ | Genomic DNA |