1VKF | pdb_00001vkf

CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1vkfd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	GlpP-like	GlpP-like	Glycerol uptake operon antiterminator-related protein TM1436	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1vkfc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	GlpP-like	GlpP-like	Glycerol uptake operon antiterminator-related protein TM1436	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vkfb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	GlpP-like	GlpP-like	Glycerol uptake operon antiterminator-related protein TM1436	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1vkfa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	GlpP-like	GlpP-like	Glycerol uptake operon antiterminator-related protein TM1436	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	GlpP-like	8041378	3000631	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GlpP-like	8041378	3000631	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GlpP-like	8041378	3000631	SCOP2B (2022-06-29)
A	SCOP2 Family	GlpP-like	8028999	4001974	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GlpP-like	8041378	3000631	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	e1vkfD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
C	e1vkfC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
B	e1vkfB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
A	e1vkfA1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: G3P_antiterm	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04309	Glycerol-3-phosphate responsive antiterminator (G3P_antiterm)	Glycerol-3-phosphate responsive antiterminator	Intracellular glycerol is usually converted to glycerol-3-phosphate in an ATP-requiring phosphorylation reaction catalysed by glycerol kinase (GlpK) glycerol-3-phosphate activates the antiterminator GlpP [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	glycerol uptake operon antiterminator-related protein	-	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process carbohydrate metabolic process polyol metabolic process alcohol metabolic process small molecule metabolic process glycerol metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR006699	Glycerol uptake operon antiterminator	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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