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 5BPD | pdb_00005bpd

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

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DPCIe5bpdD1 A: alpha arraysX: Cytidine deaminase-likeH: Ribonuclease H-likeT: Ribonuclease H-likeF: PCIECOD (v295.2)
CPCIe5bpdC1 A: alpha arraysX: Cytidine deaminase-likeH: Ribonuclease H-likeT: Ribonuclease H-likeF: PCIECOD (v295.2)
BPCIe5bpdB1 A: alpha arraysX: Cytidine deaminase-likeH: Ribonuclease H-likeT: Ribonuclease H-likeF: PCIECOD (v295.2)
APCIe5bpdA1 A: alpha arraysX: Cytidine deaminase-likeH: Ribonuclease H-likeT: Ribonuclease H-likeF: PCIECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
D1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
D3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease Chain ACATH (4.3.0)
C1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
C3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease Chain ACATH (4.3.0)
B1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
B3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease Chain ACATH (4.3.0)
A1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
A3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease Chain ACATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF01978Sugar-specific transcriptional regulator TrmB (TrmB)Sugar-specific transcriptional regulator TrmBOne 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
PF11495Transcriptional regulator TrmB, EBD N-terminal subdomaim (TrmB_EBD_N)Transcriptional regulator TrmB, EBD N-terminal subdomaimTrmB 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

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D
IPR051797Transcription regulator TrmB-likeFamily
A, B, C, D
IPR021586Transcription regulator TrmB, C-terminalDomain
A, B, C, D
IPR053499HTH-type TrmB transcriptional regulatorFamily
A, B, C, D
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
A, B, C, D
IPR002831Transcription regulator TrmB, N-terminalDomain
A, B, C, D
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily