1VLY | pdb_00001vly

Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution

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	d1vlya1	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	Aminomethyltransferase beta-barrel domain	Hypothetical protein YgfZ, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1vlya2	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	Hypothetical protein YgfZ, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8056086	4000062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8056087	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8056088	3000024	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	PRK09559	e1vlyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PRK09559	ECOD (1.6)
A	Sortase	e1vlyA3	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: Sortase	ECOD (1.6)
A	UNK_F_TYPE	e1vlyA4	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1630	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
A	2.40.30.160	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21130	YgfZ, beta-barrel domain (YgfZ_barrel)	YgfZ, beta-barrel domain	YgfZ is a folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs [1,2]. It consists of a folate-binding domain at the N-terminal (Pfam:PF01571) and a six-stranded antiparallel beta-barrel at the C-te ...	YgfZ is a folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs [1,2]. It consists of a folate-binding domain at the N-terminal (Pfam:PF01571) and a six-stranded antiparallel beta-barrel at the C-terminal, represented in this entry, with identical topology found at the C-terminal of elongation factors Tu and eEF-1alpha and in the gamma subunit of the initiation factor eIF2 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Unknown protein from 2D-page	vitamin binding organic acid binding binding ion binding modified amino acid binding folic acid binding anion binding carboxylic acid binding heterocyclic compound binding small molecule binding	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular component organization or biogenesis RNA modification macromolecule modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023758	tRNA-modifying protein YgfZ	Family
A	IPR017703	YgfZ/CAF17, C-terminal	Domain
A	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A	IPR045179	YgfZ/GcvT	Family
A	IPR048451	tRNA-modifying protein YgfZ-like, beta-barrel 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.