1VLY | pdb_00001vly

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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyGcvT aminomethyltransferase-like 8056086 4000062 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyFolate-binding domain-like 8056087 3000025 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyAminomethyltransferase beta-barrel domain-like 8056088 3000024 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APRK09559e1vlyA1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Aminomethyltransferase beta-barrel domainF: PRK09559ECOD (1.6)
ASortasee1vlyA3 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: SortaseECOD (1.6)
AUNK_F_TYPEe1vlyA4 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: UNK_F_TYPEECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.70.1630 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits CATH (4.2.0)
A3.30.70.1400 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Aminomethyltransferase beta-barrel domainsCATH (4.2.0)
A2.40.30.160 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF21130YgfZ, beta-barrel domain (YgfZ_barrel)YgfZ, beta-barrel domainYgfZ 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
PF01571GCVT N-terminal domain (GCV_T)GCVT N-terminal domainThis entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical ...This entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical processes, mainly on the degradation and transformation of small molecules. A significant function of these proteins is their role in the glycine cleavage system, which is responsible for the degradation of glycine. This system is composed of four proteins: P, T, L, and H. These proteins also participate in the demethylation of compounds such as N,N-dimethylglycine and sarcosine, converting them into simpler molecules like sarcosine and glycine, respectively. Additionally, they are involved in the catabolism of compounds like syringate and vanillate, contributing to the breakdown and assimilation of these molecules. GCVT proteins also include proteins that regulate enzymatic activity, such as the pyruvate dehydrogenase phosphatase regulatory subunit, which modulates sensitivity to magnesium ions [1-2].
Domain