5JLT | pdb_00005jlt

The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif

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)
D	SCOP2B Superfamily	DNA-binding C-terminal domain of the transcription factor MotA	8037972	3000763	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA-binding C-terminal domain of the transcription factor MotA	8037972	3000763	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA-binding C-terminal domain of the transcription factor MotA	8037972	3000763	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding C-terminal domain of the transcription factor MotA	8037972	3000763	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)
D	ProQ	e5jltD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: ProQ	ECOD (v294.1)
C	ProQ	e5jltC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: ProQ	ECOD (v294.1)
B	ProQ	e5jltB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: ProQ	ECOD (v294.1)
A	ProQ	e5jltA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: ProQ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1150.20	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription regulator MotA, C-terminal domain	CATH (4.3.0)
C	3.90.1150.20	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription regulator MotA, C-terminal domain	CATH (4.3.0)
B	3.90.1150.20	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription regulator MotA, C-terminal domain	CATH (4.3.0)
A	3.90.1150.20	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Transcription regulator MotA, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF09158	Bacteriophage T4 MotA, C-terminal (MotCF)	Bacteriophage T4 MotA, C-terminal	Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the th ...	Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, G	DNA (5'-D(GPTPGPGPAPTPTPAPTPTPAPAPGPCPAPAPAPGPCPTPTPC)-3')	-	-	-
E, H	DNA (5'-D(GPAPAPGPCPTPTPTPGPCPTPTPAPAPTPAPAPTPCPCPAPC)-3')	-	-	-
A, B, C, D	Middle transcription regulatory protein motA	DNA binding binding nucleic acid binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036474	Transcription regulator MotA, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR015241	Transcription regulator MotA, C-terminal	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR015198	Bacteriophage T4, MotA, transcription regulator N-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.