Annotations: 5BPI

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)
A	YkuD	e5bpiA1	A: beta barrels	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.2)
B	YkuD	e5bpiB1	A: beta barrels	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.2)
C	YkuD	e5bpiC1	A: beta barrels	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.2)
D	YkuD	e5bpiD1	A: beta barrels	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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	Transcriptional regulator TrmB, EBD N-terminal subdomaim (TrmB_EBD_N)	Transcriptional regulator TrmB, EBD N-terminal subdomaim	TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus [1]. TrmB has lost its DNA binding domain but retaine ...	TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus [1]. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif [1]. The sugar-binding domain (EBD) consists of two subdomains, N- and C-terminal. This entry represents the N-terminal subdomain [2], which adops a phospholiase D-like fold. The sugar binding site is on the surface of the cleft between the two subdomains. TrmBL2 lacks the C-terminal subdomain [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	DNA (5'-D(PTPAPTPAPTPCPAPTPCPGPAPTPAPGPTPGPAPTPAPTP*A)-3')	-	-	-
F	DNA (5'-D(PTPAPTPAPTPCPAPCPTPAPTPCPGPAPTPGPAPTPAPTP*A)-3')	-	-	-
A, B, C, D	TrmBL2	DNA binding binding nucleic acid binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	-

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

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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.