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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC KLHXK1 IN CRYSTAL FORM XI WITH GLUCOSE BOUND (CLOSED STATE)
 
Authors :  E. B. Kuettner, K. Kettner, A. Keim, T. M. Kriegel, N. Strater
Date :  03 Aug 10  (Deposition) - 13 Oct 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Rnaseh-Like Fold, Hexokinase, Glycolysis, Glucose Repression, Atp Binding, Mig1 Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. B. Kuettner, K. Kettner, A. Keim, D. I. Svergun, D. Volke, D. Singer, R. Hoffmann, E. C. Muller, A. Otto, T. M. Kriegel, N. Strater
Crystal Structure Of Hexokinase Klhxk1 Of Kluyveromyces Lactis: A Molecular Basis For Understanding The Control Of Yeast Hexokinase Functions Via Covalent Modification And Oligomerization.
J. Biol. Chem. V. 285 41019 2010
PubMed-ID: 20943665  |  Reference-DOI: 10.1074/JBC.M110.185850
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEXOKINASE
    ChainsA
    EC Number2.7.1.1
    EngineeredYES
    Expression SystemKLUYVEROMYCES LACTIS
    Expression System PlasmidPTSRAG5
    Expression System StrainJA6-DELTA-RAG5
    Expression System Taxid28985
    Expression System Vector TypePTS32X
    GeneKLLA0D11352G, RAG5
    Organism CommonYEAST
    Organism ScientificKLUYVEROMYCES LACTIS
    Organism Taxid28985
    StrainCBS2359/152

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CL4Ligand/IonCHLORIDE ION
3GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:157 , TYR A:158 , PRO A:159 , THR A:174 , LYS A:175 , ASN A:209 , ASP A:210 , ILE A:230 , GLY A:234 , VAL A:235 , ASN A:236 , GLU A:268 , GLN A:298 , GLU A:301 , HOH A:634 , HOH A:702BINDING SITE FOR RESIDUE GLC A 486
2AC2SOFTWARESER A:157 , TYR A:158 , PRO A:159 , THR A:174 , LYS A:175 , ASN A:209 , ASP A:210 , THR A:211 , ILE A:230 , GLY A:234 , ASN A:236 , GLU A:268 , GLU A:301 , HOH A:702BINDING SITE FOR RESIDUE BGC A 487
3AC3SOFTWARELYS A:226 , ARG A:294 , LYS A:409 , THR A:410BINDING SITE FOR RESIDUE CL A 488
4AC4SOFTWAREASN A:22 , HOH A:608BINDING SITE FOR RESIDUE CL A 489
5AC5SOFTWARELYS A:248BINDING SITE FOR RESIDUE CL A 490
6AC6SOFTWARELEU A:33 , THR A:282 , LYS A:283 , HOH A:849 , HOH A:915BINDING SITE FOR RESIDUE CL A 491

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O8M)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXOKINASE_2PS51748 Hexokinase domain profile.HXK_KLULA21-468  1A:21-468
2HEXOKINASE_1PS00378 Hexokinase domain signature.HXK_KLULA152-177  1A:152-177

(-) Exons   (0, 0)

(no "Exon" information available for 3O8M)

(-) 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:472
 aligned with HXK_KLULA | P33284 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:472
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483  
            HXK_KLULA    14 GSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
               SCOP domains d3o8ma1 A:14-223 automated matches                                                                                                                                                                                d3o8ma2 A:224-485 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Hexokinase_1-3o8mA01 A:21-222                                                                                                                                                                             -Hexokinase_2-3o8mA02 A:224-472                                                                                                                                                                                                                           ------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ee...........eeeeeeeee...eeeeeeeeee....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...ee.......ee...............hhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhhhhhh...........eeeee.hhhhh.........hhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhh.hhhhhhhhhhhhhhh....hhhhh.eeeee.....hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------HEXOKINASE_2  PDB: A:21-468 UniProt: 21-468                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------HEXOKINASE_1              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o8m A  14 GSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483  

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O8M)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HXK_KLULA | P33284)
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:0005536    glucose binding    Interacting selectively and non-covalently with the D- or L-enantiomer of glucose.
    GO:0004396    hexokinase activity    Catalysis of the reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    GO:0001678    cellular glucose homeostasis    A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0019318    hexose metabolic process    The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the 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: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.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HXK_KLULA | P332843o08 3o1b 3o1w 3o4w 3o5b 3o6w 3o80 4jax

(-) Related Entries Specified in the PDB File

3o08 CRYSTAL FORM I OF KLHXK1 (DIMER)
3o1b CRYSTAL FORM II OF KLHXK1 (DIMER)
3o1w CRYSTAL FORM III OF KLHXK1 (DIMER)
3o4w CRYSTAL FORM IV OF KLHXK1 (DIMER)
3o5b CRYSTAL FORM VII OF KLHXK1 (DIMER) WITH GLUCOSE BOUND
3o6w CRYSTAL FORM VIII OF KLHXK1 (MONOMER)
3o80 CRYSTAL FORM IX OF KLHXK1 (MONOMER)