6GFM | pdb_00006gfm

Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d6gfma2	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d6gfma1	Alpha and beta proteins (a+b)	Ferredoxin-like	DUF4478 domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d6gfma3	Membrane and cell surface proteins and peptides	Anoctamin (TMEM16)-like	DUF3412 domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d6gfma4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	AAA_31	e6gfmA1	A: alpha bundles	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: AAA_31	ECOD (develop294)
A	Ald_deCOase	e6gfmA2	A: alpha bundles	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Ald_deCOase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1850.10	Alpha Beta	2-Layer Sandwich	MCP/YpsA-like	MoCo carrier protein-like	CATH (utative)
A	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF11892	Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal (PpnN_C)	Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal	-	Family
A	PF14793	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (DUF4478)	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases	This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose ...	This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates [1]. It is found in association with Pfam:PF03641 and Pfam:PF11892.	Domain
A	PF03641	Possible lysine decarboxylase (Lysine_decarbox)	Possible lysine decarboxylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity, acting on glycosyl bonds pyrimidine-5'-nucleotide nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity inosinate nucleosidase activity AMP nucleosidase activity identical protein binding protein binding	protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR037153	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily	Homologous Superfamily
A	IPR031100	LOG family	Family
A	IPR052341	LOG family pyrimidine/purine nucleotide 5'-monophosphatases	Family
A	IPR021826	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain	Domain
A	IPR049788	Nucleotide 5'-monophosphate nucleosidase PpnN	Family
A	IPR027820	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.