1ZVV | pdb_00001zvv

Crystal structure of a ccpa-crh-dna complex

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth A]	d1zvva1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D [auth A]	d1zvva2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F [auth B]	d1zvvb1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F [auth B]	d1zvvb2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H [auth G]	d1zvvg1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Glucose-resistance amylase regulator CcpA, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H [auth G]	d1zvvg2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Glucose-resistance amylase regulator CcpA, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E [auth W]	d1zvvw_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Crh, catabolite repression HPr-like protein	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G [auth P]	d1zvvp_	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Crh, catabolite repression HPr-like protein	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
I [auth J]	d1zvvj1	Alpha and beta proteins (a+b)	HPr-like	HPr-like	HPr-like	Crh, catabolite repression HPr-like protein	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth W]	SCOP2B Superfamily	HPr-like	8036440	3000259	SCOP2B (2022-06-29)
G [auth P]	SCOP2B Superfamily	HPr-like	8036440	3000259	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	HPr-like	8036440	3000259	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)
D [auth A]		e1zvvA3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T:	F:	ECOD (20:10:01)
D [auth A]		e1zvvA2	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Nop	F:	ECOD (20:10:01)
F [auth B]		e1zvvB3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T:	F:	ECOD (20:10:01)
F [auth B]		e1zvvB1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Nop	F:	ECOD (20:10:01)
H [auth G]		e1zvvG3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T:	F:	ECOD (20:10:01)
H [auth G]		e1zvvG2	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Nop	F:	ECOD (20:10:01)
E [auth W]		e1zvvW1	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: Propep_M14	F:	ECOD (20:10:01)
G [auth P]		e1zvvP1	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: Propep_M14	F:	ECOD (20:10:01)
I [auth J]		e1zvvJ1	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: Propep_M14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
D [auth A]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F [auth B]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
F [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
H [auth G]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
H [auth G]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E [auth W]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)
G [auth P]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)
I [auth J]	3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], F [auth B], H [auth G]	PF13377	Periplasmic binding protein-like domain (Peripla_BP_3)	Periplasmic binding protein-like domain	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule liga ...	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
D [auth A], F [auth B], H [auth G]	PF00356	Bacterial regulatory proteins, lacI family (LacI)	Bacterial regulatory proteins, lacI family		Domain
E [auth W], G [auth P], I [auth J]	PF00381	PTS HPr component phosphorylation site (PTS-HPr)	PTS HPr component phosphorylation site		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth O], B [auth T], C [auth R]	DNA recognition strand CRE	-	-	-
D [auth A], F [auth B], H [auth G]	Glucose-resistance amylase regulator	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA-binding transcription repressor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	protein-containing complex protein-DNA complex
E [auth W], G [auth P], I [auth J]	HPr-like protein crh	-	import into cell phosphoenolpyruvate-dependent sugar phosphotransferase system transport import across plasma membrane carbohydrate import across plasma membrane carbohydrate transport establishment of localization transmembrane transport localization cellular process carbohydrate transmembrane transport	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], F [auth B], H [auth G]	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain	Domain
D [auth A], F [auth B], H [auth G]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
D [auth A], F [auth B], H [auth G]	IPR006377	Catabolite control protein A	Family
D [auth A], F [auth B], H [auth G]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily
D [auth A], F [auth B], H [auth G]	IPR000843	LacI-type HTH domain	Domain
E [auth W], G [auth P], I [auth J]	IPR000032	Phosphocarrier protein HPr-like	Domain
E [auth W], G [auth P], I [auth J]	IPR002114	Phosphotransferase system, HPr serine phosphorylation site	PTM
E [auth W], G [auth P], I [auth J]	IPR050399	Phosphocarrier protein HPr	Family
E [auth W], G [auth P], I [auth J]	IPR035895	HPr-like superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth W], G [auth P], I [auth J]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.