5BPD | pdb_00005bpd

Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	TrmB	e5bpdD2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TrmB	ECOD (1.6)
D	Regulator_TrmB_N	e5bpdD1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Regulator_TrmB_N	ECOD (1.6)
C	TrmB	e5bpdC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TrmB	ECOD (1.6)
C	Regulator_TrmB_N	e5bpdC1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Regulator_TrmB_N	ECOD (1.6)
B	TrmB	e5bpdB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TrmB	ECOD (1.6)
B	Regulator_TrmB_N	e5bpdB1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Regulator_TrmB_N	ECOD (1.6)
A	TrmB	e5bpdA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TrmB	ECOD (1.6)
A	Regulator_TrmB_N	e5bpdA1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Regulator_TrmB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
D	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
C	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)
C	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
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	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	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	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01978	Sugar-specific transcriptional regulator TrmB (TrmB)	Sugar-specific transcriptional regulator TrmB	One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter [2] in Thermococcus litoralis.	Domain
A, B, C, D	PF11495	Archaeal transcriptional regulator TrmB (Regulator_TrmB)	Archaeal transcriptional regulator TrmB	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (5'-D(PTPAPTPAPTPCPAPCPTPAPTPCPGPAPTPGPAPTPAPTP*A)-3')	-	-	-
E	DNA (5'-D(PTPAPTPAPTPCPAPTPCPGPAPTPAPGPTPGPAPTPAPTP*A)-3')	-	-	-
A, B, C, D	TrmBL2	DNA binding binding nucleic acid binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051797	Transcription regulator TrmB-like	Family
A, B, C, D	IPR021586	Transcription regulator TrmB, C-terminal	Domain
A, B, C, D	IPR053499	HTH-type TrmB transcriptional regulator	Family
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR002831	Transcription regulator TrmB, N-terminal	Domain
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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.