2Q07 | pdb_00002q07

Crystal structure of AF0587, a protein of unknown function

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	d2q07a1	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Uncharacterized protein AF0587	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d2q07a2	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	AF0587 domain-like	Uncharacterized protein AF0587	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d2q07a3	Alpha and beta proteins (a+b)	Cystatin-like	Pre-PUA domain	AF0587 pre C-terminal domain-like	Uncharacterized protein AF0587	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PUA domain	8023797	4003536	SCOP2 (2022-06-29)
A	SCOP2 Family	AF0587 domain-like	8023799	4002102	SCOP2 (2022-06-29)
A	SCOP2 Family	AF0587 pre C-terminal domain-like	8023800	4001697	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PUA domain-like	8036177	3001015	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Uracil-DNA glycosylase-like	8036179	3001106	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pre-PUA domain	8036180	3001126	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)
A	PUA	e2q07A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A	COG1549_like	e2q07A2	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: COG1549_like	ECOD (1.6)
A	COG1549	e2q07A3	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: COG1549	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10630	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Uracil-DNA glycosylase-like	CATH (4.3.0)
A	3.10.450.90	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22176	AF_0587-like, pre-PUA domain (AF_0587-like_pre-PUA)	AF_0587-like, pre-PUA domain	This domain is found in AF_0587 from Archaeoglobus fulgidus. It is found N-terminal to the PUA domain (Pfam:PF01472).	Domain
A	PF01472	PUA domain (PUA)	PUA domain	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modificatio ...	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Uncharacterized protein AF0587	RNA binding binding nucleic acid binding	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015947	PUA-like superfamily	Homologous Superfamily
A	IPR050076	Archaeosine Synthase Type 1/Queuine TRNA-Ribosyltransferase	Family
A	IPR054032	AF_0587-like, pre-PUA domain	Domain
A	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A	IPR036974	PUA domain superfamily	Homologous Superfamily
A	IPR038250	TGT, patch-forming C2 domain superfamily	Homologous Superfamily
A	IPR040777	Domain of unknown function DUF5591	Domain
A	IPR036511	Queuine tRNA-ribosyltransferase-like	Homologous Superfamily
A	IPR002616	tRNA-guanine(15) transglycosylase-like	Domain
A	IPR053418	Archaeosine Synthase Type 1	Family
A	IPR002478	PUA domain	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.