1KQ3

CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION

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	d1kq3a1	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	Iron-containing alcohol dehydrogenase	Glycerol dehydrogenase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1kq3a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Iron-containing alcohol dehydrogenase	8026000	4003591	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dehydroquinate synthase-like	8038379	3001905	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	Fe-ADH_2	e1kq3A1	A: alpha bundles	X: alpha-helical domain in dehydroquinate synthase-like enzymes (From Topology)	H: alpha-helical domain in dehydroquinate synthase-like enzymes (From Topology)	T: alpha-helical domain in dehydroquinate synthase-like enzymes	F: Fe-ADH_2	ECOD (1.6)
A	Fe-ADH_N	e1kq3A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Rossmann-like domain in dehydroquinate synthase-like enzymes	F: Fe-ADH_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00465	Iron-containing alcohol dehydrogenase (Fe-ADH)	Iron-containing alcohol dehydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	glycerol dehydrogenase	cation binding ion binding binding metal ion 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 glycerol dehydrogenase [NAD(P)+] activity catalytic activity glycerol dehydrogenase (NAD+) activity	alcohol catabolic process catabolic process energy derivation by oxidation of organic compounds organic hydroxy compound metabolic process carbohydrate catabolic process alcohol metabolic process fermentation glycerol catabolic process small molecule metabolic process carbohydrate metabolic process polyol metabolic process cellular metabolic process polyol catabolic process primary metabolic process alcohol catabolic process catabolic process energy derivation by oxidation of organic compounds organic hydroxy compound metabolic process carbohydrate catabolic process alcohol metabolic process fermentation glycerol catabolic process small molecule metabolic process carbohydrate metabolic process polyol metabolic process cellular metabolic process polyol catabolic process primary metabolic process generation of precursor metabolites and energy alditol catabolic process glycerol metabolic process anaerobic glycerol catabolic process alditol metabolic process organic hydroxy compound catabolic process non-glycolytic fermentation metabolic process cellular process small molecule catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016205	Glycerol dehydrogenase	Family
A	IPR018211	Alcohol dehydrogenase, iron-type, conserved site	Conserved Site
A	IPR001670	Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	glycerol dehydrogenase M-CSA #312	Glycerol dehydrogenase catalyses the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). This reaction allows microorganisms to utilise glycerol as a source of carbon under anaerobic conditions.	Defined by 4 residues: ASP:A-181 [auth A-169]HIS:A-264 [auth A-252]HIS:A-267 [auth A-255]HIS:A-281 [auth A-269] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.6 (UniProt) Search M-CSA Motif + EC 1.1.1.6

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.