3ZCB | pdb_00003zcb

VbhT Fic protein from Bartonella schoenbuchensis in complex with VbhA antitoxin mutant E24G and ATP

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	Fic-like	8063336	3001922	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)
B	VbhA_like	e3zcbB1	A: alpha bundles	X: Antitoxin VbhA (From Topology)	H: Antitoxin VbhA (From Topology)	T: Antitoxin VbhA	F: VbhA_like	ECOD (1.6)
A	Fic	e3zcbA1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: Fic	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.8.1050	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF18495	Antitoxin VbhA (VbhA)	Antitoxin VbhA	VbhT is a bacterial Fic protein of the mammalian pathogen B. schoenbuchensis7,8. It is composed of an N-terminal FIC domain and a C-terminal BID domain. FIC domains are known to catalyse adenylylation (also called AMPylation). This entry represents V ...	VbhT is a bacterial Fic protein of the mammalian pathogen B. schoenbuchensis7,8. It is composed of an N-terminal FIC domain and a C-terminal BID domain. FIC domains are known to catalyse adenylylation (also called AMPylation). This entry represents VbhA, an antitoxin that binds FIC domain (filamentation induced by cyclic AMP) of VbhT and inhibits its activity. It inhibits the adenylylation activity of VbhT by positioning close to the putative ATP-binding site, hence competing with ATP binding [1].	Domain
A	PF02661	Fic/DOC family (Fic)	Fic/DOC family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	ANTITOXIN VBHA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	regulation of cellular process regulation of protein modification process negative regulation of protein adenylylation negative regulation of biological process regulation of protein adenylylation regulation of primary metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein adenylylation regulation of cellular process regulation of protein modification process negative regulation of protein adenylylation negative regulation of biological process regulation of protein adenylylation regulation of primary metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein adenylylation regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein nucleotidylation macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of metabolic process	-
A	ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE VBHT	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding identical protein binding protein binding protein homodimerization activity protein dimerization activity adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity AMPylase activity transferase activity, transferring phosphorus-containing groups	regulation of biological process regulation of cellular process biological regulation cellular process cell division regulation of cell division protein nucleotidylation protein adenylylation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR041535	Antitoxin VbhA	Domain
B	IPR043038	Antitoxin VbhA domain superfamily	Homologous Superfamily
B	IPR033788	Antitoxin VbhA-like	Domain
A	IPR041533	Bartonella effector protein, BID domain	Domain
A	IPR036597	Fido-like domain superfamily	Homologous Superfamily
A	IPR003812	Fido 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.