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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF DESK IN COMPLEX WITH ATP
 
Authors :  F. Trajtenberg, A. Buschiazzo
Date :  12 Sep 08  (Deposition) - 15 Sep 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Ghl Atpase Domain, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Trajtenberg, M. Grana, N. Ruetalo, H. Botti, A. Buschiazzo
Structural And Enzymatic Insights Into The Atp Binding And Autophosphorylation Mechanism Of A Sensor Histidine Kinase
J. Biol. Chem. V. 285 24892 2010
PubMed-ID: 20507988  |  Reference-DOI: 10.1074/JBC.M110.147843
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SENSOR KINASE (YOCF PROTEIN)
    ChainsA
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE32
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentATP-BINDING DOMAIN
    GeneYOCF
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymDESK HISTIDINE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2IOD12Ligand/IonIODIDE ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:38 , HOH A:72 , HOH A:84 , HOH A:124 , HOH A:165 , GLU A:289 , ASN A:293 , LYS A:296 , 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:359 , MG A:371 , HOH A:373 , HOH A:374 , HOH A:382BINDING SITE FOR RESIDUE ATP A 1
02AC2SOFTWAREATP A:1 , HOH A:165 , GLU A:289 , ASN A:293BINDING SITE FOR RESIDUE MG A 371
03AC3SOFTWAREARG A:341BINDING SITE FOR RESIDUE IOD A 2
04AC4SOFTWARESER A:319BINDING SITE FOR RESIDUE IOD A 3
05AC5SOFTWAREHOH A:109 , GLY A:243 , ASN A:281BINDING SITE FOR RESIDUE IOD A 5
06AC6SOFTWAREGLU A:327BINDING SITE FOR RESIDUE IOD A 6
07AC7SOFTWAREHOH A:123 , HOH A:136 , HOH A:137BINDING SITE FOR RESIDUE IOD A 7
08AC8SOFTWAREHOH A:18 , HOH A:83 , ARG A:343BINDING SITE FOR RESIDUE IOD A 8
09AC9SOFTWARESER A:276BINDING SITE FOR RESIDUE IOD A 9
10BC1SOFTWAREHOH A:108BINDING SITE FOR RESIDUE IOD A 10
11BC2SOFTWARETRP A:311 , GLU A:342BINDING SITE FOR RESIDUE IOD A 11
12BC3SOFTWAREGLU A:328 , SER A:330BINDING SITE FOR RESIDUE IOD A 12

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EHG)

(-) 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:125
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:125
                                   252       262       272       282       292       302       312       322       332       342       352       362     
           DESK_BACSU   243 GIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPN 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee..............hhhhhhhhhhhhh..eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehg A 243 GIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPN 367
                                   252       262       272       282       292       302       312       322       332       342       352       362     

   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 3EHG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3ehf 3ehh 3ehj