7EGS

The crystal structure of lobe domain of E. coli RNA polymerase complexed with the C-terminal domain of UvrD

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	F_UNCLASSIFIED	e7egsA2	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF04561	e7egsA1	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: PF04561	ECOD (1.6)
B	PF21196	e7egsB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF21196	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
A	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
B	PF21196	PcrA/UvrD tudor domain (PcrA_UvrD_tudor)	PcrA/UvrD tudor domain	The PcrA/UvrD helicase binds directly to RNA polymerase (RNAP). This entry represents the C-terminal tudor domain that mediates interaction with RNA polymerase [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed RNA polymerase subunit beta	ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to chemical response to antibiotic cellular response to stimulus cellular response to stress response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation oxoacid metabolic process organic acid metabolic process reactive nitrogen species metabolic process nitrogen cycle metabolic process small molecule metabolic process nitrate metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B	DNA helicase II	ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity DNA translocase activity isomerase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides single-stranded DNA helicase activity 3'-5' DNA helicase activity	rolling circle DNA replication DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process DNA-templated DNA replication maintenance of fidelity replication fork processing cellular response to stimulus rolling circle DNA replication DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process DNA-templated DNA replication maintenance of fidelity replication fork processing cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress cellular process DNA repair response to radiation response to abiotic stimulus SOS response cellular component organization DNA duplex unwinding organelle organization DNA geometric change chromosome organization DNA conformation change cellular component organization or biogenesis mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication nucleotide-excision repair nucleotide-excision repair, DNA duplex unwinding DNA recombination recombinational repair DNA unwinding involved in DNA replication	protein-containing complex catalytic complex DNA helicase complex single-stranded DNA-dependent ATP-dependent DNA helicase complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A	IPR007642	RNA polymerase Rpb2, domain 2	Domain
A	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
A	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
A	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
A	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
A	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
A	IPR007641	RNA polymerase Rpb2, domain 7	Domain
B	IPR014017	UvrD-like DNA helicase, C-terminal	Domain
B	IPR005753	DNA helicase, ATP-dependent, UvrD type	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR014016	UvrD-like helicase, ATP-binding domain	Domain
B	IPR000212	DNA helicase, UvrD/REP type	Family
B	IPR013986	DExx box DNA helicase domain superfamily	Homologous Superfamily

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 R01GM133198.