1Z3E

Crystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1z3ea1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	ArsC-like	Regulatory protein Spx	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1z3ea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1z3eb1	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ArsC-like	8022739	4003282	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin-like	8035119	3000031	SCOP2 (2022-06-29)
B	SCOP2 Family	C-terminal domain of RNA polymerase alpha subunit	8022741	4001030	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	C-terminal domain of RNA polymerase alpha subunit	8035121	3000519	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF03960	e1z3eA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: PF03960	ECOD (1.6)
B	PF03118	e1z3eB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03960	ArsC family (ArsC)	ArsC family	-	Family
B	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)	Bacterial RNA polymerase, alpha chain C terminal domain	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. T ...	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Regulatory protein spx	-	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity
B	DNA-directed RNA polymerase alpha chain	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity 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 DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity 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	cellular biosynthetic process cellular metabolic process 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity 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
A	IPR023731	Global transcriptional regulator Spx	Family
A	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A	IPR006660	Arsenate reductase-like	Family
A	IPR006504	Transcriptional regulator Spx/MgsR	Family
B	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
B	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
B	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
B	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
B	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
B	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.