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(-) Description

Title :  X-RAY STRUCTURE OF THE HPR KINASE/PHOSPHATASE FROM STAPHYLOCOCCUS XYLOSUS AT 1.95 A RESOLUTION
 
Authors :  J. A. Marquez, S. Hasenbein, B. Koch, S. Fieulaine, S. Nessler, W. Hengstenberg, K. Scheffzek
Date :  20 Dec 01  (Deposition) - 03 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (3x)
Biol. Unit 2:  A  (3x)
Keywords :  Protein Kinase, Phosphotransfer, Protein Phosphatase, Dual Activity, Product, Substrate, Transferase, Hydrolase, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Marquez, S. Hasenbein, B. Koch, S. Fieulaine, S. Nessler, R. B. Russell, W. Hengstenberg, K. Scheffzek
Structure Of The Full-Length Hpr Kinase/Phosphatase From Staphylococcus Xylosus At 1. 95 A Resolution: Mimicking The Product/Substrate Of The Phospho Transfer Reactions.
Proc. Natl. Acad. Sci. Usa V. 99 3458 2002
PubMed-ID: 11904409  |  Reference-DOI: 10.1073/PNAS.052461499
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HPR KINASE/PHOSPHATASE
    ChainsA, B
    EC Number2.7.1.-, 3.1.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A (NOVAGEN)
    Expression System StrainBL21(DE3) (STRATAGENE)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHPRK
    Organism ScientificSTAPHYLOCOCCUS XYLOSUS
    Organism Taxid1288

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x) B
Biological Unit 2 (3x)A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:33 , THR A:55 , THR A:56 , ARG A:88 , THR A:114 , HOH A:329 , TYR B:45 , ARG B:49BINDING SITE FOR RESIDUE PO4 A 315
2AC2SOFTWAREARG A:49 , ARG A:250 , ARG B:33 , THR B:55 , THR B:56 , ARG B:88 , THR B:114 , HOH B:319BINDING SITE FOR RESIDUE PO4 B 315
3AC3SOFTWAREGLY A:154 , ILE A:155 , GLY A:156 , LYS A:157 , SER A:158 , GLU A:159 , PO4 A:317 , HOH A:438BINDING SITE FOR RESIDUE PO4 A 316
4AC4SOFTWAREHIS A:136 , SER A:153 , GLY A:154 , LYS A:157 , PO4 A:316 , HOH A:428BINDING SITE FOR RESIDUE PO4 A 317
5AC5SOFTWAREGLY B:154 , ILE B:155 , GLY B:156 , LYS B:157 , SER B:158 , GLU B:159 , ARG B:202 , PO4 B:317 , HOH B:341BINDING SITE FOR RESIDUE PO4 B 316
6AC6SOFTWAREHIS B:136 , SER B:153 , LYS B:157 , ARG B:202 , PO4 B:316BINDING SITE FOR RESIDUE PO4 B 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KO7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KO7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KO7)

(-) Exons   (0, 0)

(no "Exon" information available for 1KO7)

(-) 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:285
 aligned with HPRK_STAXY | Q9S1H5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           HPRK_STAXY     1 MLTTKSLVERFELEMIAGEAGLNKQIKNTDISRPGLEMAGYFSHYASDRIQLLGTTELSFYNLLPDEERKGRMRKLCRPETPAIIVTRDLEPPEELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLVADDNVEIREISKDELIGRAPKLIEHLLEIRGLGIINVMTLFGAGSILTEKRLRLNIHLENWHKEKLYDRVGLNEETLRILDTEITKKTIPVRPGRNVAVIIEVAAMNYRLNIMGINTAEEFNDRLN 298
               SCOP domains d1ko7a1 A:1-129 HPr kinase/phoshatase HprK N-terminal domain                                                                     d1ko7a2 A:130-298 HPr kinase HprK C-terminal domain                                                                                                                       SCOP domains
               CATH domains 1ko7A01 A:1-129  [code=3.40.1390.20, no name defined]                                                                            1ko7A02 A:130-288 P-loop containing nucleotide triphosphate hydrolases                                                                                         ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeehhhhh........ee.hhhhhh..........eeeehhhhhhhhhhhhhhhhhhhhhhhh......eee......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeee.eeeee..eeeeeee....hhhhhhhhhhhh..eeee..eeeeee.....eeee.hhhhh.eeee...eeeehhhhhhhhhh..eee..eeeeee.-------------.eeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ko7 A   1 MLTTKSLVERFELEMIAGEAGLNKQIKNTDISRPGLEMAGYFSHYASDRIQLLGTTELSFYNLLPDEERKGRMRKLCRPETPAIIVTRDLEPPEELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLVADDNVEIREISKDELIGRAPKLIEHLLEIRGLGIINVMTLFGAGSILTEKRLRLNIHLEN-------------EETLRILDTEITKKTIPVRPGRNVAVIIEVAAMNYRLNIMGINTAEEFNDRLN 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |       -     | 250       260       270       280       290        
                                                                                                                                                                                                                                                                 232           246                                                    

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with HPRK_STAXY | Q9S1H5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           HPRK_STAXY     1 MLTTKSLVERFELEMIAGEAGLNKQIKNTDISRPGLEMAGYFSHYASDRIQLLGTTELSFYNLLPDEERKGRMRKLCRPETPAIIVTRDLEPPEELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLVADDNVEIREISKDELIGRAPKLIEHLLEIRGLGIINVMTLFGAGSILTEKRLRLNIHLENWHKEKLYDRVGLNEETLRILDTEITKKTIPVRPGRNVAVIIEVAAMNYRLNIMGINTAEEFNDRLN 298
               SCOP domains d1ko7b1 B:1-129 HPr kinase/phoshatase HprK N-terminal domain                                                                     d1ko7b2 B:130-298 HPr kinase HprK C-terminal domain                                                                                                                       SCOP domains
               CATH domains 1ko7B01 B:1-128  [code=3.40.1390.20, no name defined]                                                                           -1ko7B02 B:130-288 P-loop containing nucleotide triphosphate hydrolases                                                                                         ---------- CATH domains
           Pfam domains (1) Hpr_kinase_N-1ko7B01 B:1-126                                                                                                  Hpr_kinase_C-1ko7B03 B:127-297                                                                                                                                             - Pfam domains (1)
           Pfam domains (2) Hpr_kinase_N-1ko7B02 B:1-126                                                                                                  Hpr_kinase_C-1ko7B04 B:127-297                                                                                                                                             - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhh.eeeehhhhh........ee.hhhhhh..........eeeehhhhhhhhh..hhhhhhhhhhhhh......eee......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeee.eeeee..eeeeeee....hhhhhhhhhhhh..eeee..eeeeeeee..eeeee.hhhhh.eeee...eeeehhhhhhhhhh..eee..eeeeee.-------------.eeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ko7 B   1 MLTTKSLVERFELEMIAGEAGLNKQIKNTDISRPGLEMAGYFSHYASDRIQLLGTTELSFYNLLPDEERKGRMRKLCRPETPAIIVTRDLEPPEELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLVADDNVEIREISKDELIGRAPKLIEHLLEIRGLGIINVMTLFGAGSILTEKRLRLNIHLEN-------------EETLRILDTEITKKTIPVRPGRNVAVIIEVAAMNYRLNIMGINTAEEFNDRLN 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |       -     | 250       260       270       280       290        
                                                                                                                                                                                                                                                                 232           246                                                    

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HPRK_STAXY | Q9S1H5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006109    regulation of carbohydrate metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
    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: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.

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