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 DESKC-H188V IN COMPLEX WITH AMP-PCP
 
Authors :  D. Albanesi, P. M. Alzari, A. Buschiazzo
Date :  12 Sep 08  (Deposition) - 15 Sep 09  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Four-Helix Bundle, Ghl Atpase Domain, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Albanesi, M. Martin, F. Trajtenberg, M. C. Mansilla, A. Haouz, P. M. Alzari, D. De Mendoza, A. Buschiazzo
Structural Plasticity And Catalysis Regulation Of A Thermosensor Histidine Kinase
Proc. Natl. Acad. Sci. Usa V. 106 16185 2009
PubMed-ID: 19805278  |  Reference-DOI: 10.1073/PNAS.0906699106

(-) Compounds

Molecule 1 - SENSOR KINASE (YOCF PROTEIN)
    ChainsA, B
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE32
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentENTIRE CYTOPLASMIC REGION
    GeneYOCF
    MutationYES
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymDESK HISTIDINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CA2Ligand/IonCALCIUM ION
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECA A:1 , HOH A:8 , HOH A:55 , GLU A:289 , ASN A:293 , HIS A:297 , SER A:298 , ASP A:320 , THR A:323 , PHE A:324 , LYS A:325 , GLY A:326 , HIS A:335 , GLY A:336 , LEU A:337 , THR A:359BINDING SITE FOR RESIDUE ACP A 1303
2AC2SOFTWAREGLU A:289 , ASN A:293 , ACP A:1303BINDING SITE FOR RESIDUE CA A 1
3AC3SOFTWARECA B:1 , HOH B:2 , HOH B:19 , HOH B:38 , GLU B:289 , ASN B:293 , HIS B:297 , SER B:298 , ASP B:320 , THR B:323 , PHE B:324 , LYS B:325 , GLY B:326 , HIS B:335 , GLY B:336 , LEU B:337 , THR B:359BINDING SITE FOR RESIDUE ACP B 1303
4AC4SOFTWAREHOH B:19 , GLU B:289 , ASN B:293 , ACP B:1303BINDING SITE FOR RESIDUE CA B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EHJ)

(-) 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:203
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:206
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
           DESK_BACSU   163 KLEDANERIAELVKLEERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPNN 368
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee...........---hhhhhhhhhhhhh..eeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehj A 163 KLEDANERIAELVKLEERQRmARDLVDTLGQKLSLmGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSmKGIRLKDELINIKQILEAADImFIYEEEKWPENISLLNENILSmCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSF---HGLLGmRERLEFANGSLHIDTENGTKLTmAIPNN 368
                                   172       182|      192     | 202       212       222       232       242       252       262|      272       282  |    292       302       312       322        |-  |    342       352       362|     
                                              183-MSE        198-MSE                                    241-MSE               263-MSE               285-MSE                                       331 335    |                    363-MSE 
                                                                                                                                                                                                           340-MSE                        

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:214
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365    
           DESK_BACSU   156 ERERLEEKLEDANERIAELVKLEERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPNNS 369
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee...........---hhhhhhhhhhhhh..eeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehj B 156 ERERLEEKLEDANERIAELVKLEERQRmARDLVDTLGQKLSLmGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSmKGIRLKDELINIKQILEAADImFIYEEEKWPENISLLNENILSmCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSF---HGLLGmRERLEFANGSLHIDTENGTKLTmAIPNNS 369
                                   165       175       185       195  |    205       215       225       235     | 245       255       265       275       285       295       305       315       325     | 335    |  345       355       365    
                                                     183-MSE        198-MSE                                    241-MSE               263-MSE               285-MSE                                       331 335    |                    363-MSE  
                                                                                                                                                                                                                  340-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 3EHJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DESK_BACSU | O34757)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
    ACP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ehj)
 

(-) 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
  3ehj
    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
  DESK_BACSU | O34757
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.13.3
    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
  DESK_BACSU | O34757
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DESK_BACSU | O347573ehf 3ehg 3ehh 3gie 3gif 3gig 5iuj 5iuk 5iul 5ium 5iun

(-) Related Entries Specified in the PDB File

3ehf 3ehg 3ehh