Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CRA TRANSCRIPTIONAL DUAL REGULATOR FROM PSEUDOMONAS PUTIDA
 
Authors :  M. Chavarria, C. Santiago, R. Platero, T. Krell, J. M. Casasnovas, V. De
Date :  30 Jul 10  (Deposition) - 12 Jan 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dual Transcriptional Regulator, Dna, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Chavarria, C. Santiago, R. Platero, T. Krell, J. M. Casasnovas, V. De Lorenzo
Fructose 1-Phosphate Is The Preferred Effector Of The Metabolic Regulator Cra Of Pseudomonas Putida
J. Biol. Chem. V. 286 9351 2011
PubMed-ID: 21239488  |  Reference-DOI: 10.1074/JBC.M110.187583

(-) Compounds

Molecule 1 - FRUCTOSE TRANSPORT SYSTEM REPRESSOR FRUR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneECK0081
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid160488
    StrainKT2440
    SynonymCRA TRANSCRIPTIONAL DUAL REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:49 , ASN A:73 , TYR A:76 , ASP A:148 , ARG A:149 , SER A:247BINDING SITE FOR RESIDUE GOL A 332
2AC2SOFTWAREASN B:73 , TYR B:76 , ASP B:148 , ARG B:149 , ARG B:197 , SER B:247 , HOH B:362 , HOH B:379BINDING SITE FOR RESIDUE GOL B 332

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O74)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O74)

(-) Exons   (0, 0)

(no "Exon" information available for 3O74)

(-) Sequences/Alignments

Asymmetric/Biological 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:270
 aligned with Q88PQ6_PSEPK | Q88PQ6 from UniProtKB/TrEMBL  Length:331

    Alignment length:270
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
         Q88PQ6_PSEPK    60 HTRTLGFILPDLENPSYARIAKQLEQGARARGYQLLIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRRYQGEAFSRECGQRLMQQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQLGTFGDNQLLDFLPLPVNAMAQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQRIS 329
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee........hhhhhhhhh...eeee.........eeeeehhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh....eeeee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o74 A  60 HTRTLGFILPDLENPSYARIAKQLEQGARARGYQLLIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRRYQGEAFSRECGQRLmQQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQLGTFGDNQLLDFLPLPVNAmAQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQRIS 329
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
                                                                                                                                                                                                   229-MSE                                                     289-MSE                                    

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q88PQ6_PSEPK | Q88PQ6 from UniProtKB/TrEMBL  Length:331

    Alignment length:271
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329 
         Q88PQ6_PSEPK    60 HTRTLGFILPDLENPSYARIAKQLEQGARARGYQLLIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRRYQGEAFSRECGQRLMQQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQLGTFGDNQLLDFLPLPVNAMAQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQRISV 330
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peripla_BP_1-3o74B01 B:61-268                                                                                                                                                                                   -------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Peripla_BP_1-3o74B02 B:61-268                                                                                                                                                                                   -------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee........hhhhhhhhh...eeee.........eeeeehhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh.......eeeee..hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhh.....eeeee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o74 B  60 HTRTLGFILPDLENPSYARIAKQLEQGARARGYQLLIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRRYQGEAFSRECGQRLmQQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQLGTFGDNQLLDFLPLPVNAmAQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQRISV 330
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329 
                                                                                                                                                                                                   229-MSE                                                     289-MSE                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 3O74)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O74)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q88PQ6_PSEPK | Q88PQ6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009750    response to fructose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fructose stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o74)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3o74
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q88PQ6_PSEPK | Q88PQ6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q88PQ6_PSEPK | Q88PQ6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q88PQ6_PSEPK | Q88PQ63o75

(-) Related Entries Specified in the PDB File

3o75 SAME PROTEIN IN COMPLEX WITH BETA-D-FRUCTOSE 1-PHOSPHATE