2YJT

Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

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)
C	d2yjtc_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	RraA-like	RraA-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2yjta_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	RraA-like	RraA-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2yjtb_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	RraA-like	RraA-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d2yjtd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	RraA-like	8039820	3000324	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RraA-like	8039820	3000324	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RraA-like	8039820	3000324	SCOP2B (2022-06-29)
D	SCOP2 Family	Tandem AAA-ATPase domain	8076571	4000282	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	RecA-like P-loop NTPases	8076572	3002019	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)
C	PF03737	e2yjtC1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF03737	ECOD (1.6)
A	PF03737	e2yjtA1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF03737	ECOD (1.6)
B	PF03737	e2yjtB1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF03737	ECOD (1.6)
D	PF00271	e2yjtD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.50.30.40	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	3.50.30.40	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
B	3.50.30.40	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF03737	Aldolase/RraA (RraA-like)	Aldolase/RraA	-	Family
D	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	REGULATOR OF RIBONUCLEASE ACTIVITY A	enzyme regulator activity molecular function inhibitor activity molecular function regulator activity nuclease inhibitor activity enzyme inhibitor activity endoribonuclease inhibitor activity ribonuclease inhibitor activity protein binding binding enzyme binding identical protein binding	protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis catabolic process negative regulation of biological process RNA metabolic process protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process organic substance metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of RNA catabolic process primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process negative regulation of RNA metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex
D	ATP-DEPENDENT RNA HELICASE SRMB	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 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 ATP-dependent activity, acting on RNA ATP-dependent activity RNA binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding 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 catalytic activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity RNA strand annealing activity annealing activity	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis 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 nucleobase-containing compound metabolic process positive regulation of metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis 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 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 regulation of nucleobase-containing compound metabolic process cellular component disassembly regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression 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 positive regulation of cellular component organization regulation of cellular component organization cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process transcriptional attenuation DNA-templated transcription termination positive regulation of termination of DNA-templated transcription RNA biosynthetic process cellular component organization nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of protein-containing complex disassembly positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of RNA biosynthetic 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 negative regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR005493	Ribonuclease E inhibitor RraA/RraA-like protein	Family
A, B, C	IPR010203	Regulator of ribonuclease activity A	Family
A, B, C	IPR014339	Regulator of ribonuclease activity A, gammaproteobacteria	Family
A, B, C	IPR036704	Ribonuclease E inhibitor RraA/RraA-like superfamily	Homologous Superfamily
D	IPR001650	Helicase, C-terminal domain-like	Domain
D	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D	IPR028621	ATP-dependent RNA helicase SrmB	Family
D	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
D	IPR011545	DEAD/DEAH box helicase domain	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.