1DLI

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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyUDP-glucose/GDP-mannose dehydrogenase-like8001154 4000109 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyUDP-glucose/GDP-mannose dehydrogenase C-terminal domain-like8056190 3000011 SCOP2 (2022-06-29)
ASCOP2 Superfamily6-phosphogluconate dehydrogenase-like8001155 3000048 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AUDPG_MGDP_dhe1dliA1 A: alpha arraysX: 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-likeF: UDPG_MGDP_dhECOD (1.6)
ANAD_Gly3P_dh_Ne1dliA2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_Gly3P_dh_NECOD (1.6)
AUDPG_MGDP_dh_Ce1dliA3 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: UDPG/MGDP dehydrogenase C-terminal domainF: UDPG_MGDP_dh_CECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
A1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03720UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain (UDPG_MGDP_dh_C)UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domainThe 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
PF03721UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain (UDPG_MGDP_dh_N)UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domainThe 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
PF00984UDP-glucose/GDP-mannose dehydrogenase family, central domain (UDPG_MGDP_dh)UDP-glucose/GDP-mannose dehydrogenase family, central domainThe 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
UDP-GLUCOSE DEHYDROGENASE -

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

ChainsEnzyme NameDescriptionCatalytic Residues
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
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