3QOQ | pdb_00003qoq

Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Arc	e3qoqD2	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Arc	ECOD (1.6)
C	Arc	e3qoqC2	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Arc	ECOD (1.6)
B	Arc	e3qoqB2	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Arc	ECOD (1.6)
A	Arc	e3qoqA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Arc	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
C	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
B	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
A	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03869	Arc-like DNA binding domain (Arc)	Arc-like DNA binding domain	Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (5'-D(TPGPCPCPGPGPCPGPTPTPTPTPGPCPCPAPGPT)-3')	-	-	-
E	DNA (5'-D(APCPTPGPGPCPAPAPAPAPCPGPCPCPGPGPCPA)-3')	-	-	-
A, B, C, D	Alginate and motility regulator Z	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor 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 cell aggregation biofilm formation regulation of single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation on inanimate substrate biological process involved in intraspecies interaction between organisms positive regulation of biological process single-species biofilm formation single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation regulation of single-species biofilm formation single-species submerged biofilm formation positive regulation of cellular process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process regulation of polysaccharide metabolic process polysaccharide metabolic process regulation of polysaccharide biosynthetic process regulation of carbohydrate biosynthetic process regulation of carbohydrate metabolic process type IV pilus-dependent motility cell motility organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular component organization or biogenesis cell projection assembly positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility locomotion regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility negative regulation of cell motility bacterial-type flagellum-dependent cell motility negative regulation of bacterial-type flagellum-dependent cell motility negative regulation of single-species biofilm formation negative regulation of single-species biofilm formation on inanimate substrate	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR005569	Arc-like DNA binding domain	Domain

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.