6VCL

Crystal structure of E.coli RppH-DapF in complex with pppGpp, Mg2+ and F-

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	d6vcla1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d6vcla3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
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)
A	PF01678	e6vclA1	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: PF01678	ECOD (1.6)
B	PF00293	e6vclB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B	PF00293	NUDIX domain (NUDIX)	NUDIX domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Diaminopimelate epimerase	racemase activity, acting on amino acids and derivatives 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 racemase activity, acting on amino acids and derivatives 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 cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process organic substance metabolic process organic substance biosynthetic process lysine metabolic process oxoacid metabolic process cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process diaminopimelate metabolic process fatty acid derivative metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process lipid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
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	catabolic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process catabolic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process regulation of biosynthetic process RNA destabilization positive regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process positive regulation of catabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process negative regulation of biological process negative regulation of cellular metabolic 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 cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process NAD-cap decapping RNA decapping tRNA metabolic process tRNA processing ncRNA metabolic process RNA processing	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001653	Diaminopimelate epimerase, DapF	Family
A	IPR018510	Diaminopimelate epimerase, active site	Active Site
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

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.