2FF4 | pdb_00002ff4

Mycobacterium tuberculosis EmbR in complex with low affinity phosphopeptide

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2ff4b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	PhoB-like	Probable regulatory protein EmbR	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d2ff4b2	All alpha proteins	alpha-alpha superhelix	TPR-like	BTAD-like	Probable regulatory protein EmbR, middle domain	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d2ff4b3	All beta proteins	SMAD/FHA domain	SMAD/FHA domain	FHA domain	Probable regulatory protein EmbR, C-terminal domain	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d2ff4a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	PhoB-like	Probable regulatory protein EmbR	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d2ff4a2	All alpha proteins	alpha-alpha superhelix	TPR-like	BTAD-like	Probable regulatory protein EmbR, middle domain	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d2ff4a3	All beta proteins	SMAD/FHA domain	SMAD/FHA domain	FHA domain	Probable regulatory protein EmbR, C-terminal domain	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8040841	3001179	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SMAD/FHA domain-like	8040846	3000137	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TPR-like	8040843	3001345	SCOP2B (2022-06-29)
A	SCOP2 Family	PhoB-like	8028462	4000729	SCOP2 (2022-06-29)
A	SCOP2 Family	BTAD-like	8028464	4001552	SCOP2 (2022-06-29)
A	SCOP2 Family	FHA domain	8028467	4002605	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-terminal effector domain of the bipartite response regulators	8040841	3001179	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TPR-like	8040843	3001345	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SMAD/FHA domain-like	8040846	3000137	SCOP2 (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	Ricin_B_lectin, RicinB_lectin_2	e2ff4B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Ricin_B_lectin, RicinB_lectin_2	ECOD (v294.1)
B	Phage_CII	e2ff4B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (v294.1)
B		e2ff4B3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
A	FHA	e2ff4A1	A: beta sandwiches	X: SMAD/FHA domain	H: SMAD/FHA domain	T: SMAD/FHA domain	F: FHA	ECOD (v294.1)
A	Trans_reg_C	e2ff4A2	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Trans_reg_C	ECOD (v294.1)
A	BTAD	e2ff4A3	A: alpha bundles	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: BTAD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
B	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
A	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03704	Bacterial transcriptional activator domain (BTAD)	Bacterial transcriptional activator domain	-	Repeat
A, B	PF00486	Transcriptional regulatory protein, C terminal (Trans_reg_C)	Transcriptional regulatory protein, C terminal		Domain
A, B	PF00498	FHA domain (FHA)	FHA domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	DNA repair protein RAD9	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding binding histone binding DNA binding double-stranded DNA binding nucleic acid binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair nucleotide-excision repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair nucleotide-excision repair double-strand break repair DNA damage checkpoint signaling regulation of cellular process regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle mitotic intra-S DNA damage checkpoint signaling regulation of cell cycle cell cycle process regulation of biological process regulation of cell cycle process biological regulation DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage DNA-templated DNA replication maintenance of fidelity regulation of primary metabolic process negative regulation of DNA-templated DNA replication regulation of DNA strand resection involved in replication fork processing DNA strand resection involved in replication fork processing negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA strand resection involved in replication fork processing regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication negative regulation of DNA replication negative regulation of metabolic process regulation of macromolecule metabolic process DNA replication regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of metabolic process replication fork processing regulation of DNA metabolic process regulation of DNA replication regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle G1/S phase transition regulation of mitotic cell cycle phase transition mitotic G1 DNA damage checkpoint signaling regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle site of DNA damage
A, B	Probable regulatory protein embR	DNA binding binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity GTPase activity	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of 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	cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure extracellular region cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F]	IPR047249	TP53-binding protein 1-like, first BRCT domain	Domain
C [auth E], D [auth F]	IPR013914	Rad9-like Rad53-binding domain, fungi	Domain
C [auth E], D [auth F]	IPR047252	TP53-binding protein 1-like	Family
C [auth E], D [auth F]	IPR001357	BRCT domain	Domain
C [auth E], D [auth F]	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, B	IPR005158	Bacterial transcriptional activator domain	Domain
A, B	IPR001867	OmpR/PhoB-type DNA-binding domain	Domain
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR000253	Forkhead-associated (FHA) domain	Domain
A, B	IPR051677	AfsR/DnrI/RedD regulatory protein	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth E], D [auth F]	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.