1WPK | pdb_00001wpk

Methylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ada DNA repair protein, N-terminal domain (N-Ada 10)	8035698	3001437	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	HTH_AraC_1	e1wpkA4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AraC_1	ECOD (1.6)
A	Ada_Zn_binding	e1wpkA3	A: few secondary structure elements	X: Ada DNA repair protein, N-terminal domain (N-Ada 10) (From Topology)	H: Ada DNA repair protein, N-terminal domain (N-Ada 10) (From Topology)	T: Ada DNA repair protein, N-terminal domain (N-Ada 10)	F: Ada_Zn_binding	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.10.10	Alpha Beta	3-Layer(aba) Sandwich	DNA Methylphosphotriester Repair Domain	DNA Methylphosphotriester Repair Domain	CATH (4.3.0)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02805	Metal binding domain of Ada (Ada_Zn_binding)	Metal binding domain of Ada	-	Family
A	PF00165	Bacterial regulatory helix-turn-helix proteins, AraC family (HTH_AraC)	Bacterial regulatory helix-turn-helix proteins, AraC family	In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind ove ...	In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ADA regulatory protein	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process methylation DNA metabolic process DNA alkylation repair DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008332	Methylguanine DNA methyltransferase, ribonuclease-like domain	Domain
A	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A	IPR018060	AraC-like, DNA binding HTH domain	Domain
A	IPR036217	Methylated DNA-protein cysteine methyltransferase, DNA binding domain	Homologous Superfamily
A	IPR035451	Ada-like domain superfamily	Homologous Superfamily
A	IPR018062	HTH domain AraC-type, conserved site	Conserved Site
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR036631	Methylated DNA-protein cysteine methyltransferase domain superfamily	Homologous Superfamily
A	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding	Domain
A	IPR001497	Methylated-DNA-[protein]-cysteine S-methyltransferase, active site	Active Site
A	IPR016221	Bifunctional regulatory protein Ada	Family
A	IPR004026	Ada DNA repair, metal-binding	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SMC	Parent Component: CYS RESID: AA0234 PSI-MOD : S-methyl-L-cysteine MOD:00239

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.