1DLI

THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION

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	d1dlia1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	UDP-glucose dehydrogenase (UDPGDH), middle domain	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
A	d1dlia2	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	UDP-glucose dehydrogenase (UDPGDH)	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
A	d1dlia3	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	UDP-glucose dehydrogenase (UDPGDH), C-terminal (UDP-binding) domain	(Streptococcus pyogenes ) [TaxId: 1314 ],	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	8001154	4000109	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8001155	3000048	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like	8056190	3000011	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	UDPG_MGDP_dh	e1dliA1	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	NAD_Gly3P_dh_N	e1dliA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_Gly3P_dh_N	ECOD (1.6)
A	UDPG_MGDP_dh_C	e1dliA3	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	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	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	UDP-GLUCOSE DEHYDROGENASE	NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding 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 UDP-glucose 6-dehydrogenase activity catalytic activity	oxoacid metabolic process UDP-glucuronate metabolic process cellular biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process UDP-glucuronate biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide-sugar biosynthetic process oxoacid metabolic process UDP-glucuronate metabolic process cellular biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process UDP-glucuronate biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide-sugar biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process small molecule biosynthetic process cellular metabolic process nucleotide-sugar metabolic process carboxylic acid metabolic process primary metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process macromolecule biosynthetic process polysaccharide metabolic process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028357	UDP-glucose 6-dehydrogenase, bacterial type	Family
A	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A	IPR017476	UDP-glucose/GDP-mannose dehydrogenase	Family
A	IPR014026	UDP-glucose/GDP-mannose dehydrogenase, dimerisation	Domain
A	IPR014027	UDP-glucose/GDP-mannose dehydrogenase, C-terminal	Domain
A	IPR036220	UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A	IPR001732	UDP-glucose/GDP-mannose dehydrogenase, N-terminal	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	UDP-glucose 6-dehydrogenase M-CSA #92	Bacterial UDP-glucose dehydrogenase is essential for the formation of the antiphagocytic capsule that protects many virulent bacteria from the host's immune system. The homodimeric enzyme is composed of an N-terminal NAD⁺ dinucleotide binding domain and a C-terminal UDP-sugar binding domain connected by a long central alpha helix. The enzyme catalyses the NAD+ dependent oxidation of UDP-glucose to UDP-glucuronic acid. In mammals this is the substrate for UDP-glucuronosyl transferases in the liver. UDP-glucuronosyl transferases catalyse the formation of glucuronide conjugates with various substances e.g. bilirubin - aiding its excretion. The active site contains residues contributed from the N- and C-terminal domains as well as from the central alpha-helix. Thr118 from the N-terminal forms a hydrogen bond to an ordered active site water molecule, that may be critical for the catalytic mechanism. Ser117 and Pro120 are also probably essential for proper orientation of the catalytic Thr118. The central alpha-helix contributes two active site residues; Lys204 and Asn208. Glu141 forms a hydrogen bond to the key catalytic residue Lys204. The C-terminal contributes two residues; Cys260 and Asp264, both having direct roles in the enzyme mechanism.	Defined by 6 residues: THR:A-118GLU:A-145LYS:A-204ASN:A-208CYS:A-260ASP:A-264 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.22 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.22

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.