3VEX

Crystal structure of the O-carbamoyltransferase TobZ H14N variant in complex with carbamoyl adenylate intermediate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YrdC/RibB-like	8004446	3000166	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8004440	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8092399	3000092	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	Carbam_trans_C	e3vexA3	A: a+b complex topology	X: YrdC/RibB (From Topology)	H: YrdC/RibB (From Topology)	T: YrdC/RibB	F: Carbam_trans_C	ECOD (1.6)
A	Carbam_trans_N_N	e3vexA4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Carbam_trans_N_N	ECOD (1.6)
A	Carbam_trans_N_C	e3vexA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Carbam_trans_N_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.870.20	Alpha Beta	Alpha-Beta Complex	DHBP synthase	Carbamoyltransferase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16861	Carbamoyltransferase C-terminus (Carbam_trans_C)	Carbamoyltransferase C-terminus	This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6 ...	This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity [1]. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity [2], EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase [3]. These proteins contain two domains, this is the smaller, C-terminal, domain.	Domain
A	PF02543	Carbamoyltransferase N-terminus (Carbam_trans_N)	Carbamoyltransferase N-terminus	This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6 ...	This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity [1]. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity [2], EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase [3]. These proteins contain two domains, this is the larger, N-terminal, domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	O-carbamoyltransferase TobZ	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity catalytic activity ligase activity carboxyl- or carbamoyltransferase activity transferase activity, transferring one-carbon groups transferase activity cation binding transition metal ion binding iron ion binding metal ion binding	aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process glycoside metabolic process organic hydroxy compound metabolic process carbohydrate derivative metabolic process kanamycin biosynthetic process alcohol metabolic process antibiotic biosynthetic process glycoside biosynthetic process antibiotic metabolic process aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process glycoside metabolic process organic hydroxy compound metabolic process carbohydrate derivative metabolic process kanamycin biosynthetic process alcohol metabolic process antibiotic biosynthetic process glycoside biosynthetic process antibiotic metabolic process aminoglycoside antibiotic metabolic process biosynthetic process organic hydroxy compound biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process small molecule metabolic process tobramycin biosynthetic process tobramycin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038152	Carbamoyltransferase, C-terminal domain superfamily	Homologous Superfamily
A	IPR031730	Carbamoyltransferase, C-terminal	Domain
A	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A	IPR003696	Carbamoyltransferase	Domain
A	IPR051338	NodU/CmcH Carbamoyltransferase	Family

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.