9DVT | pdb_00009dvt

Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth R], E [auth S]	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain
D [auth R], E [auth S]	PF00486	Transcriptional regulatory protein, C terminal (Trans_reg_C)	Transcriptional regulatory protein, C terminal		Domain
F [auth G]	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1]	Non-template DNA	-	-	-
B [auth 2]	Template DNA	-	-	-
C [auth A]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity 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	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	cellular anatomical structure intracellular anatomical structure cytoplasm 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
D [auth R], E [auth S]	DNA-binding dual master transcriptional regulator RpaA	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 molecular transducer activity phosphorelay response regulator activity	rhythmic process circadian rhythm regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process rhythmic process circadian rhythm regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cell division circadian regulation of translation protein biosynthetic process post-transcriptional regulation of gene expression protein metabolic process regulation of protein metabolic process translation regulation of translation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex protein-DNA complex
F [auth G]	RNA polymerase sigma factor SigA1	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
C [auth A]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C [auth A]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
C [auth A]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C [auth A]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C [auth A]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
D [auth R], E [auth S]	IPR039420	Transcriptional regulatory protein WalR-like	Family
D [auth R], E [auth S]	IPR001867	OmpR/PhoB-type DNA-binding domain	Domain
D [auth R], E [auth S]	IPR011006	CheY-like superfamily	Homologous Superfamily
D [auth R], E [auth S]	IPR001789	Signal transduction response regulator, receiver domain	Domain
D [auth R], E [auth S]	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
D [auth R], E [auth S]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F [auth G]	IPR007627	RNA polymerase sigma-70 region 2	Domain
F [auth G]	IPR000943	RNA polymerase sigma-70	Domain
F [auth G]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F [auth G]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F [auth G]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F [auth G]	IPR017848	RNA polymerase sigma factor, RpoD/SigA, cyanobacteria	Family
F [auth G]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F [auth G]	IPR007630	RNA polymerase sigma-70 region 4	Domain
F [auth G]	IPR014284	RNA polymerase sigma-70-like domain	Domain
F [auth G]	IPR007624	RNA polymerase sigma-70 region 3	Domain
F [auth G]	IPR028630	RNA polymerase sigma factor RpoD	Family
F [auth G]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth R], E [auth S]	PHD	Parent Component: ASP RESID: AA0033 PSI-MOD : L-aspartic 4-phosphoric anhydride MOD:00042