4XAX | pdb_00004xax

Crystal structure of Thermus thermophilus CarD in complex with the Thermus aquaticus RNA polymerase beta1 domain

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)
B		e4xaxB1	A: Cytidine deaminase-like	X: EF-hand-related	H: EF-hand	T:	F:	ECOD (20:10:01)
A		e4xaxA1	A: Cytidine deaminase-like	X: Ribonuclease H-like	H: Ribonuclease H-like	T: ATP-synt_VA_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.10.170	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
B	1.20.58.1290	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02559	CarD-like/TRCF RID domain (CarD_TRCF_RID)	CarD-like/TRCF RID domain	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvat ...	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3].	Domain
B	PF21095	CarD, C-terminal domain (CarD_C)	CarD, C-terminal domain	This entry represents the C-terminal helical domain of CarD from Mycobacterium tuberculosis, a RNAP-binding protein that regulates transcription and essential processes [1-3]. This domain binds DNA in a non-specific manner [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	CarD	-	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process rRNA transcription metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process	-
A	DNA-directed RNA polymerase subunit beta domain 1	DNA binding binding nucleic acid binding DNA-directed 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 ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR042215	CarD-like, C-terminal domain	Homologous Superfamily
B	IPR048792	CarD, C-terminal domain	Domain
B	IPR052531	CarD-like transcription regulator	Family
B	IPR036101	CarD-like/TRCF, RNAP-interacting domain superfamily	Homologous Superfamily
B	IPR003711	CarD-like/TRCF, RNAP-interacting domain	Domain
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	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
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

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.