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 :  STRUCTURE OF PHOP FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. Menon, S. Wang
Date :  08 Mar 11  (Deposition) - 13 Jul 11  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha Fold, Winged Helix-Turn-Helix, Transcription Regulator, Dna Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Menon, S. Wang
Structure Of The Response Regulator Phop From Mycobacterium Tuberculosis Reveals A Dimer Through The Receiver Domain.
Biochemistry V. 50 5948 2011
PubMed-ID: 21634789  |  Reference-DOI: 10.1021/BI2005575

(-) Compounds

Molecule 1 - POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePHOP, RV0757
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    StrainH37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2MSO2Mod. Amino AcidSELENOMETHIONINE SELENOXIDE
3PGR1Ligand/IonR-1,2-PROPANEDIOL
4SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:180 , ARG B:183 , ARG B:204 , HOH B:260BINDING SITE FOR RESIDUE SO4 B 301
2AC2SOFTWARETYR A:48 , THR A:49 , ARG A:59BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARETYR B:48 , THR B:49 , ARG B:59BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWARESER B:194 , ARG B:244BINDING SITE FOR RESIDUE SO4 B 304
5AC5SOFTWARETHR A:180 , ARG A:183 , ARG A:204 , HOH A:253 , HOH A:287BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWARELYS B:195 , ARG B:237 , GLY B:238BINDING SITE FOR RESIDUE PGR B 248

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R0J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:121 -Pro A:122
2Lys B:121 -Pro B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R0J)

(-) Exons   (0, 0)

(no "Exon" information available for 3R0J)

(-) 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:224
 aligned with P71814_MYCTU | P71814 from UniProtKB/TrEMBL  Length:247

    Alignment length:230
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
         P71814_MYCTU    17 TTPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVMMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGKGNKEPRNVRLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDTGEKRLLHTLRGVGYVLREP 246
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh.....eeeee...hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhh.------..eeee..eeee.....eee..eee..hhhhhhhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhh......eeee...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0j A  17 TTPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVmmPGmDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGK------NVRLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDTGEKRLLHTLRGVGYVLREP 246
                                    26        36        46        56        66      ||76|       86        96       106       116       126       136    |    - |     156       166       176       186       196       206       216       226       236       246
                                                                                   73-MSO                                                             141    148                                                                                                  
                                                                                    74-MSE                                                                                                                                                                        
                                                                                       77-MSE                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with P71814_MYCTU | P71814 from UniProtKB/TrEMBL  Length:247

    Alignment length:229
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
         P71814_MYCTU    18 TPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVMMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGKGNKEPRNVRLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDTGEKRLLHTLRGVGYVLREP 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh.--------.eee..eee......eee..eee..hhhhhhhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhh......eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0j B  18 TPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVmmPGmDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGK--------RLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDTGEKRLLHTLRGVGYVLREP 246
                                    27        37        47        57        67     || 77        87        97       107       117       127       137   |     -  |    157       167       177       187       197       207       217       227       237         
                                                                                  73-MSO                                                             141      150                                                                                                
                                                                                   74-MSE                                                                                                                                                                        
                                                                                      77-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 3R0J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R0J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R0J)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P71814_MYCTU | P71814)
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:0009247    glycolipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0046889    positive regulation of lipid biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0044315    protein secretion by the type VII secretion system    The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type VII protein secretion system.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:121 - Pro A:122   [ RasMol ]  
    Lys B:121 - Pro B:122   [ RasMol ]  
 

(-) 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
  3r0j
    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
  P71814_MYCTU | P71814
    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
  P71814_MYCTU | P71814
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        P71814_MYCTU | P718142pmu
UniProtKB/TrEMBL
        P71814_MYCTU | P718145ed4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R0J)