1DB3

E.COLI GDP-MANNOSE 4,6-DEHYDRATASE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1db3a_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Tyrosine-dependent oxidoreductases	GDP-mannose 4,6-dehydratase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8058099	4000088	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SDR-like	8058100	3000038	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GDP_Man_Dehyd	e1db3A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16363	GDP-mannose 4,6 dehydratase (GDP_Man_Dehyd)	GDP-mannose 4,6 dehydratase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GDP-MANNOSE 4,6-DEHYDRATASE	NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding identical protein binding protein binding protein homodimerization activity NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity GDP-mannose 4,6-dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	nucleoside phosphate metabolic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process GDP-mannose metabolic process carbohydrate derivative biosynthetic process nucleoside phosphate metabolic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process GDP-mannose metabolic process carbohydrate derivative biosynthetic process 'de novo' GDP-L-fucose biosynthetic process GDP-L-fucose metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleotide-sugar biosynthetic process GDP-L-fucose biosynthetic process colanic acid metabolic process macromolecule metabolic process macromolecule biosynthetic process colanic acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR016040	NAD(P)-binding domain	Domain
A	IPR006368	GDP-mannose 4,6-dehydratase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	GDP-mannose 4,6-dehydratase M-CSA #487	GDP-mannose 4,6-dehydratase (GMD) catalyses the conversion of GDP-mannose to GDP-4-dehydro-6deoxy-D-mannose in the first and regulatory step in the de novo biosynthesis of GDP-fucose. Fucose is distributed widely in the glycoconjugates of species ranging from bacteria to humans. Once synthesised it is incorporated into glycoconjugates by specific fucosyltransferases that use GDP-fucose as the fucose donor. Important glycoconjugates include the cell wall polysaccharides of bacteria that confer pathogenicity, components of mammal antigens and perhaps the best known example, the human blood group antigens. Defects in GMD activity provide insight into the diverse roles that fucose plays in biology and hence the importance of the enzyme. For example in plants, defects in GMD result in altered shoot development whilst in humans defects have been linked to immune disorders. Kinetic analysis of the protein gives evidence to suggest that the role of NADP⁺ does not support either of the two currently proposed mechanisms. The exact overall mechanism remains unclear.	Defined by 4 residues: THR:A-132GLU:A-134TYR:A-156LYS:A-160 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.1.47 (PDB Primary Data) Search M-CSA Motif + EC 4.2.1.47

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.