8QA8 | pdb_00008qa8

Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02195	ParB N-terminal domain (ParB_N)	ParB N-terminal domain	This entry describes the N-terminal domain of ParB proteins, predominantly found in bacteria. This domain is characterised by a highly conserved arginine motif, RRXR, known as the arginine patch, which is crucial for ParB DNA binding activity [1-2]. ...	This entry describes the N-terminal domain of ParB proteins, predominantly found in bacteria. This domain is characterised by a highly conserved arginine motif, RRXR, known as the arginine patch, which is crucial for ParB DNA binding activity [1-2]. ParB plays a vital role in chromosome partitioning and nucleoid occlusion. These proteins are essential for ensuring proper chromosome segregation during cell division by binding to the DNA origin of replication and localising to both poles of the predivisional cell following DNA replication. ParB comprises three highly conserved domains: an N-terminal nucleotide-binding domain (NBD), a central helix-turn-helix (HTH) parS-binding domain, a non-structured linker region, and a C-terminal dimerisation domain that tightly links the two subunits of the ParB dimer [3]. ParB proteins share significant sequence and structural similarity with Sulfiredoxin (Srx), a sulfinic acid reductase identified in eukaryotes. Sequence comparison and phylogenetic analysis of the Srx and ParB protein families suggest that Srx evolved via truncation of ParB, resulting in the removal of the entire C-terminal half of the protein including the HTH domain [4].	Domain
A, B, C, D, E A, B, C, D, E, F	PF08535	KorB domain (KorB)	KorB domain	This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal ...	This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon [1]. This domain includes the DNA-binding HTH motif [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Transcriptional repressor protein KorB	DNA binding binding nucleic acid binding identical protein binding protein binding	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 cycle chromosome segregation cell cycle process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR037048	KorB, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR042075	KorB DNA-binding domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036086	ParB/Sulfiredoxin superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050336	Chromosome-partitioning and nucleoid occlusion protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR008988	Transcriptional repressor, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010575	KorB, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003115	ParB-like, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013741	Repressor KorB domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004437	ParB/RepB/Spo0J partition protein	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.