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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUGAR BINDING DOMAIN OF THE ARCHAEAL TRANSCRIPTIONAL REGULATOR TRMB
 
Authors :  M. Krug, S. J. Lee, K. Diederichs, W. Boos, W. Welte
Date :  27 Nov 05  (Deposition) - 21 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Sugar-Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Krug, S. J. Lee, K. Diederichs, W. Boos, W. Welte
Crystal Structure Of The Sugar Binding Domain Of The Archaeal Transcriptional Regulator Trmb
J. Biol. Chem. V. 281 10976 2006
PubMed-ID: 16473881  |  Reference-DOI: 10.1074/JBC.M512809200

(-) Compounds

Molecule 1 - ARCHAEAL TRANSCRIPTIONAL REGULATOR TRMB
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSL152
    Expression System Strain: SF120
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 110-338
    Organism Scientific: THERMOCOCCUS LITORALIS
    Organism Taxid: 2265

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (2x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2MAL1Ligand/IonMALTOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2MAL2Ligand/IonMALTOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN X:189 , HIS X:190 , ASN X:205 , TYR X:228 , SER X:229 , GLU X:302 , ALA X:303 , VAL X:304 , ASN X:305 , GLY X:320 , MET X:321 , PHE X:322 , ALA X:323 , VAL X:324 , ILE X:325 , GLU X:326 , HOH X:350 , HOH X:351 , HOH X:352BINDING SITE FOR RESIDUE MAL X 343
2AC2SOFTWARELEU X:281 , GLU X:282 , VAL X:324 , GLU X:326 , ARG X:341 , SER X:342 , HOH X:447BINDING SITE FOR RESIDUE IMD X 344

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F5T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr X:186 -Lys X:187
2Ser X:210 -Ile X:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F5T)

(-) Exons   (0, 0)

(no "Exon" information available for 2F5T)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain X from PDB  Type:PROTEIN  Length:233
 aligned with TRMBR_THELN | Q7LYW4 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:233
                                                                                                                                                                                                                                                              338    
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        |-   
          TRMBR_THELN   110 AIWRSRSFDEAIEMFRESLYSAKNEVIVVTPSEFFETIREDLIKTLERGVTVSLYIDKIPDLSEFKGKGNFFVRQFYKLNHLIGMTDGKEVVTIQNATFDSIGPPSFKSTYPEIIFSQYSLIIEIFKESTLEKEIIGNPKDIRFFAMFHAVDFVKNHLKNRNIYAEITGKNLESGRLETLTGRVVGYTLSLREAVNNIHLETENGVVKVGGMFAVIEDYESTEIKFIMG----   -
               SCOP domains d2f5tx2 X:110-246 Transcriptional regulator TrmB                                                                                         d2f5tx1 X:247-338 Transcriptional regulator TrmB                                            ---- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh...eeeeee......eeeee...eeeee...........eeee.hhhhhhhhhhhhhhhhhh.eeeeeee.....eee.hhhhhhhhhhhhh....eeeeeeeee.....eeeeeeeeeeeeee....eeeeeeee..eeeeee........eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f5t X 110 AIWRSRSFDEAIEMFRESLYSAKNEVIVVTPSEFFETIREDLIKTLERGVTVSLYIDKIPDLSEFKGKGNFFVRQFYKLNHLIGMTDGKEVVTIQNATFDSIGPPSFKSTYPEIIFSQYSLIIEIFKESTLEKEIIGNPKDIRFFAMFHAVDFVKNHLKNRNIYAEITGKNLESGRLETLTGRVVGYTLSLREAVNNIHLETENGVVKVGGMFAVIEDYESTEIKFIMGGSRS 342
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F5T)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain X   (TRMBR_THELN | Q7LYW4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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