6D1V | pdb_00006d1v

Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	MutT-like	8061706	4001887	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Nudix	8061707	3000098	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nudix	8061703	3000098	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e6d1vB1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleotidyltransferase	T: DEAD	F:	ECOD (20:10:01)
A		e6d1vA1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleotidyltransferase	T: DEAD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain
A	PF01678	Diaminopimelate epimerase (DAP_epimerase)	Diaminopimelate epimerase	Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	RNA (5'-D((APC))-R(PGP*U)-3')	-	-	-
B	RNA pyrophosphohydrolase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity mRNA 5'-diphosphatase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity mRNA 5'-diphosphatase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity RNA NAD-cap (NMN-forming) hydrolase activity	regulation of cellular process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic 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 positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of cellular process regulation of cellular process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic 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 positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of cellular process RNA catabolic process regulation of biosynthetic process RNA destabilization regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process positive regulation of catabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process mRNA metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process NAD-cap decapping RNA decapping nucleobase-containing compound biosynthetic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm
A	Diaminopimelate epimerase	isomerase activity racemase and epimerase activity diaminopimelate epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding binding protein homodimerization activity isomerase activity racemase and epimerase activity diaminopimelate epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process L-lysine biosynthetic process via diaminopimelate small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process L-lysine biosynthetic process via diaminopimelate small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR022927	RNA pyrophosphohydrolase RppH	Family
B	IPR000086	NUDIX hydrolase domain	Domain
B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
B	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
B	IPR020476	NUDIX hydrolase	Domain
A	IPR001653	Diaminopimelate epimerase, DapF	Family
A	IPR018510	Diaminopimelate epimerase, active site	Active Site

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.