1YRW | pdb_00001yrw

Crystal Structure of E.coli ArnA Transformylase Domain

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	d1yrwa1	All beta proteins	FMT C-terminal domain-like	FMT C-terminal domain-like	Post formyltransferase domain	Polymyxin resistance protein ArnA, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1yrwa2	Alpha and beta proteins (a/b)	Formyltransferase	Formyltransferase	Formyltransferase	Polymyxin resistance protein ArnA, 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	SCOP2B Superfamily	Formyltransferase	8057772	3000030	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FMT C-terminal domain-like	8057773	3000015	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		e1yrwA1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Autotransporter	F:	ECOD (20:10:01)
A		e1yrwA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.170	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Formyl transferase, N-terminal domain	CATH (4.3.0)
A	3.10.25.10	Alpha Beta	Roll	Methionyl-tRNA Fmet Formyltransferase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02911	Formyl transferase, C-terminal domain (Formyl_trans_C)	Formyl transferase, C-terminal domain		Domain
A	PF00551	Formyl transferase (Formyl_trans_N)	Formyl transferase	This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces ...	This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	protein ArnA	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding carboxy-lyase activity lyase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity UDP-glucuronate decarboxylase activity transferase activity, transferring one-carbon groups UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors UDP-glucuronate dehydrogenase activity identical protein binding protein binding	carbohydrate derivative biosynthetic process lipooligosaccharide metabolic process glycolipid metabolic process lipid A biosynthetic process liposaccharide metabolic process carbohydrate derivative metabolic process lipid biosynthetic process primary metabolic process glycolipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process lipid A metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process carbohydrate derivative biosynthetic process lipooligosaccharide metabolic process glycolipid metabolic process lipid A biosynthetic process liposaccharide metabolic process carbohydrate derivative metabolic process lipid biosynthetic process primary metabolic process glycolipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process lipid A metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process lipooligosaccharide biosynthetic process metabolic process cellular process phosphorus metabolic process lipid metabolic process response to stimulus response to chemical response to antibiotic lipopolysaccharide biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process macromolecule metabolic process nucleoside phosphate metabolic process nucleotide-sugar metabolic process UDP-D-xylose metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process small molecule metabolic process UDP-D-xylose biosynthetic process nucleotide-sugar biosynthetic process amino sugar biosynthetic process UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process amino sugar metabolic process	cellular anatomical structure membrane protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050177	Bifunctional lipid A modification and metabolic enzymes	Family
A	IPR045869	Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs	Domain
A	IPR036477	Formyl transferase, N-terminal domain superfamily	Homologous Superfamily
A	IPR021168	Bifunctional polymyxin resistance protein, ArnA	Family
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR001509	NAD-dependent epimerase/dehydratase	Domain
A	IPR002376	Formyl transferase, N-terminal	Domain
A	IPR005793	Formyl transferase, C-terminal	Domain
A	IPR011034	Formyl transferase-like, C-terminal domain superfamily	Homologous Superfamily

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.