Annotations: 5B88

RRM-like domain of DEAD-box protein, CsdA

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	PrpF	e5b88A1	A: beta barrels	X: beta-Grasp	H: Diaminopimelate epimerase-like	T: Diaminopimelate epimerase-like	F: PrpF	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03880	DbpA RNA binding domain (DbpA)	DbpA RNA binding domain	This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack spe ...	This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ATP-dependent RNA helicase DeaD	RNA strand annealing activity RNA binding nucleic acid conformation isomerase activity isomerase activity binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid nucleic acid binding single-stranded RNA binding annealing activity macromolecular conformation isomerase activity catalytic activity adenyl ribonucleotide binding nucleotide binding RNA strand annealing activity RNA binding nucleic acid conformation isomerase activity isomerase activity binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid nucleic acid binding single-stranded RNA binding annealing activity macromolecular conformation isomerase activity catalytic activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization 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 ATP-dependent activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA	response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus response to radiation regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus response to radiation regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process biological regulation negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process positive regulation of gene expression regulation of RNA stability cellular process regulation of mRNA metabolic process positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process protein metabolic process regulation of protein metabolic process translation regulation of translation cellular response to stimulus cellular response to cold cellular response to stress ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component biogenesis cellular component organization ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly cellular component organization or biogenesis ribosome assembly	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR034415	CsdA, RNA recognition motif	Domain
A	IPR057325	RNA helicase DeaD, dimerization domain	Domain
A	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A	IPR005580	DEAD box helicase DbpA/CsdA, RNA-binding domain	Domain
A	IPR050547	DEAD box ATP-dependent RNA helicases	Family
A	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A	IPR011545	DEAD/DEAH-box helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR021046	Cold-shock protein, DEAD box A, C-terminal	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR044742	RhlB-like, DEAD/DEAH-box helicase domain	Domain
A	IPR028618	ATP-dependent RNA helicase DeaD	Family

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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.

5B88 | pdb_00005b88

RRM-like domain of DEAD-box protein, CsdA

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage