1MV8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mv8a1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	GDP-mannose 6-dehydrogenase, middle domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d1mv8a2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	GDP-mannose 6-dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d1mv8a3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	GDP-mannose 6-dehydrogenase, GDP-binding domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1mv8b1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	GDP-mannose 6-dehydrogenase, middle domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1mv8b2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	GDP-mannose 6-dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1mv8b3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	GDP-mannose 6-dehydrogenase, GDP-binding domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d1mv8c1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	GDP-mannose 6-dehydrogenase, middle domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d1mv8c2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	GDP-mannose 6-dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d1mv8c3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	GDP-mannose 6-dehydrogenase, GDP-binding domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d1mv8d1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	GDP-mannose 6-dehydrogenase, middle domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d1mv8d2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	GDP-mannose 6-dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d1mv8d3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	GDP-mannose 6-dehydrogenase, GDP-binding domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	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/GDP-mannose dehydrogenase-like	8056191	4000109	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like	8056193	3000011	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8056192	3000048	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like	8056193	3000011	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8056192	3000048	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8056192	3000048	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like	8056193	3000011	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like	8056193	3000011	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8056192	3000048	SCOP2B (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	UDPG_MGDP_dh	e1mv8A1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: UDPG_MGDP_dh	ECOD (1.6)
A	ApbA	e1mv8A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ApbA	ECOD (1.6)
A	UDPG_MGDP_dh_C	e1mv8A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: UDPG/MGDP dehydrogenase C-terminal domain	F: UDPG_MGDP_dh_C	ECOD (1.6)
B	UDPG_MGDP_dh	e1mv8B1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: UDPG_MGDP_dh	ECOD (1.6)
B	ApbA	e1mv8B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ApbA	ECOD (1.6)
B	UDPG_MGDP_dh_C	e1mv8B3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: UDPG/MGDP dehydrogenase C-terminal domain	F: UDPG_MGDP_dh_C	ECOD (1.6)
C	UDPG_MGDP_dh	e1mv8C1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: UDPG_MGDP_dh	ECOD (1.6)
C	ApbA	e1mv8C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ApbA	ECOD (1.6)
C	UDPG_MGDP_dh_C	e1mv8C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: UDPG/MGDP dehydrogenase C-terminal domain	F: UDPG_MGDP_dh_C	ECOD (1.6)
D	UDPG_MGDP_dh	e1mv8D1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: UDPG_MGDP_dh	ECOD (1.6)
D	ApbA	e1mv8D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ApbA	ECOD (1.6)
D	UDPG_MGDP_dh_C	e1mv8D3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: UDPG/MGDP dehydrogenase C-terminal domain	F: UDPG_MGDP_dh_C	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	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03720	UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain (UDPG_MGDP_dh_C)	UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain
A, B, C, D	PF03721	UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain (UDPG_MGDP_dh_N)	UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain
A, B, C, D	PF00984	UDP-glucose/GDP-mannose dehydrogenase family, central domain (UDPG_MGDP_dh)	UDP-glucose/GDP-mannose dehydrogenase family, central domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GDP-mannose 6-dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors GDP-mannose 6-dehydrogenase activity catalytic activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding	alginic acid biosynthetic process oxoacid metabolic process cellular biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process polysaccharide metabolic process organic substance biosynthetic process small molecule metabolic process carbohydrate metabolic process small molecule biosynthetic process polysaccharide biosynthetic process cellular metabolic process alginic acid biosynthetic process oxoacid metabolic process cellular biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process polysaccharide metabolic process organic substance biosynthetic process small molecule metabolic process carbohydrate metabolic process small molecule biosynthetic process polysaccharide biosynthetic process cellular metabolic process carbohydrate biosynthetic process carboxylic acid metabolic process alginic acid metabolic process primary metabolic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus response to stress cellular response to cell envelope stress cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms response to osmotic stress response to abiotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR028358	GDP-mannose 6-dehydrogenase	Family
A, B, C, D	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR017476	UDP-glucose/GDP-mannose dehydrogenase	Family
A, B, C, D	IPR014026	UDP-glucose/GDP-mannose dehydrogenase, dimerisation	Domain
A, B, C, D	IPR014027	UDP-glucose/GDP-mannose dehydrogenase, C-terminal	Domain
A, B, C, D	IPR036220	UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR001732	UDP-glucose/GDP-mannose dehydrogenase, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.