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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF TRMB, A GLOBAL TRANSCRIPTIONAL REGULATOR OF THE HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS IN COMPLEX WITH SUCROSE
 
Authors :  M. Krug, S. -J. Lee, W. Boos, W. Welte, K. Diederichs
Date :  13 Feb 11  (Deposition) - 30 May 12  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Krug, S. J. Lee, W. Boos, K. Diederichs, W. Welte
The Three-Dimensional Structure Of Trmb, A Transcriptional Regulator Of Dual Function In The Hyperthermophilic Archaeo Pyrococcus Furiosus In Complex With Sucrose.
Protein Sci. V. 22 800 2013
PubMed-ID: 23576322  |  Reference-DOI: 10.1002/PRO.2263

(-) Compounds

Molecule 1 - TRMB, A GLOBAL TRANSCRIPTION REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PF1743
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL9Ligand/IonGLYCEROL
3SUC1Ligand/IonSUCROSE
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL18Ligand/IonGLYCEROL
3SUC2Ligand/IonSUCROSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:75 , SER A:76 , GLU A:126 , LYS A:217 , GOL A:411BINDING SITE FOR RESIDUE ACT A 401
02AC2SOFTWAREARG A:125 , TYR A:129 , ASP A:150 , THR A:154 , ARG A:157BINDING SITE FOR RESIDUE ACT A 402
03AC3SOFTWAREASN A:133 , GLU A:275 , THR A:277 , GLU A:332 , ILE A:333 , LYS A:334BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWARETHR A:277 , GLU A:329 , THR A:331 , GLU A:332 , GOL A:407BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARELEU A:188 , ASN A:189 , HIS A:190BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARELYS A:249 , LYS A:279 , PHE A:322 , ALA A:323 , GLU A:329 , GOL A:407BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREGLY A:197 , MET A:321 , GLU A:329 , GOL A:404 , GOL A:406BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWARETHR A:290 , GLY A:291 , GLU A:302 , GOL A:409BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREALA A:274 , GLU A:275 , THR A:290 , LYS A:334 , ILE A:336 , GOL A:408BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWAREGLY A:295 , TYR A:296BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWAREMET A:123 , SER A:127 , SER A:130 , GLU A:199 , LYS A:217 , ACT A:401BINDING SITE FOR RESIDUE GOL A 411
12BC3SOFTWARESER A:229 , TYR A:273 , ALA A:303 , VAL A:304 , ASN A:305 , GLY A:320 , MET A:321 , PHE A:322 , ALA A:323 , VAL A:324 , GLU A:326 , VAL A:339 , HOH A:502 , HOH A:503 , HOH A:504BINDING SITE FOR RESIDUE SUC A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QPH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:45 -Tyr A:46
2Thr A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QPH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QPH)

(-) Exons   (0, 0)

(no "Exon" information available for 3QPH)

(-) 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 A from PDB  Type:PROTEIN  Length:335
 aligned with TRMBR_PYRFU | Q9HGZ9 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:335
                                                                                                                                                                                                                                                                                                                                                                    338    
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337|    
          TRMBR_PYRFU     8 SHALSEIGFTKYEILTYWTLLVYGPSTAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEGTPKVYAAYSPRIAFFRFKKELEDIMKKLEIELNNVKKEEQRPAIWRSRSFDEAIEMFRESLYSAKNEVIVVTPSEFFETIREDLIKTLERGVTVSLYIDKIPDLSEFKGKGNFFVRQFYKLNHLIGMTDGKEVVTIQNATFDSIGPPSFKSTYPEIIFSQYSLIIEIFKESTLEKEIIGNPKDIRFFAMFHAVDFVKNHLKNRNIYAEITGKNLESGRLETLTGRVVGYTLSLREAVNNIHLETENGVVKVGGMFAVIEDYESTEIKFIMG----   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...hhhhhhhhhhhhh.............hhhhhhhhhhh.eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh...eeeeee......eeeee...eeeee...........eeee.hhhhhhhhhhhhhhhhhhheeeeeee.....eee.hhhhhhhhhhhhh....eeeeeeeee.....eeeeeeeeeeeeee....eeeeeeee..eeeeee........eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qph A   8 SHALSEIGFTKYEILTYWTLLVYGPSTAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEGTPKVYAAYSPRIAFFRFKKELEDIMKKLEIELNNVKKEEQRPAIWRSRSFDEAIEMFRESLYSAKNEVIVVTPSEFFETIREDLIKTLERGVTVSLYIDKIPDLSEFKGKGNFFVRQFYKLNHLIGMTDGKEVVTIQNATFDSIGPPSFKSTYPEIIFSQYSLIIEIFKESTLEKEIIGNPKDIRFFAMFHAVDFVKNHLKNRNIYAEITGKNLESGRLETLTGRVVGYTLSLREAVNNIHLETENGVVKVGGMFAVIEDYESTEIKFIMGVDLQ 342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3QPH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QPH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QPH)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMBR_PYRFU | Q9HGZ9)
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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