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(-) Description

Title :  CRYSTAL STRUCTURE OF DIMERIC KLHXK1 IN CRYSTAL FORM I
 
Authors :  E. B. Kuettner, K. Kettner, A. Keim, T. M. Kriegel, N. Strater
Date :  19 Jul 10  (Deposition) - 13 Oct 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
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
    Chains: A, B
    EC Number: 2.7.1.1
    Engineered: YES
    Expression System: KLUYVEROMYCES LACTIS
    Expression System Plasmid: PTSRAG5
    Expression System Strain: JA6-DELTA-RAG5
    Expression System Taxid: 28985
    Expression System Vector Type: PTS32X
    Gene: KLLA0D11352G, RAG5
    Organism Common: YEAST
    Organism Scientific: KLUYVEROMYCES LACTIS
    Organism Taxid: 28985
    Strain: CBS2359/152

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2SO422Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:232 , THR A:233 , GLY A:234 , GLY A:417 , SER A:418BINDING SITE FOR RESIDUE SO4 A 486
02AC2SOFTWARELYS A:40 , SER A:128 , LYS A:132 , VAL A:278 , PRO A:280 , HOH A:555BINDING SITE FOR RESIDUE SO4 A 487
03AC3SOFTWAREPRO A:223 , GLN A:224 , LYS A:226 , GLY A:407 , TYR A:408 , LYS A:409 , THR A:410BINDING SITE FOR RESIDUE SO4 A 488
04AC4SOFTWAREPHE A:420 , LYS A:427 , VAL A:453 , ALA A:454 , HOH A:640BINDING SITE FOR RESIDUE SO4 A 489
05AC5SOFTWAREGLY A:417 , SER A:418 , ASN A:421 , ARG A:422BINDING SITE FOR RESIDUE SO4 A 490
06AC6SOFTWAREGLN A:432 , LYS A:435BINDING SITE FOR RESIDUE SO4 A 491
07AC7SOFTWAREGLY A:88 , GLY A:89 , THR A:90 , ASN A:91BINDING SITE FOR RESIDUE SO4 A 492
08AC8SOFTWARESER A:292 , PRO A:293 , ARG A:294 , GLN A:297 , LYS A:302BINDING SITE FOR RESIDUE SO4 A 493
09AC9SOFTWARELYS A:444 , MET A:445 , HOH A:646BINDING SITE FOR RESIDUE SO4 A 494
10BC1SOFTWARETYR B:73 , LYS B:226 , TYR B:408 , SO4 B:491 , HOH B:571 , HOH B:614 , HOH B:638BINDING SITE FOR RESIDUE NHE B 486
11BC2SOFTWAREGLY B:232 , THR B:233 , GLY B:417 , SER B:418BINDING SITE FOR RESIDUE SO4 B 487
12BC3SOFTWARESER B:37 , SER B:38 , ARG B:393 , HOH B:604BINDING SITE FOR RESIDUE SO4 B 488
13BC4SOFTWAREVAL B:242 , ARG B:406BINDING SITE FOR RESIDUE SO4 B 489
14BC5SOFTWAREGLY B:417 , SER B:418 , ASN B:421 , ARG B:422BINDING SITE FOR RESIDUE SO4 B 490
15BC6SOFTWARELYS B:226 , GLY B:407 , TYR B:408 , LYS B:409 , THR B:410 , NHE B:486BINDING SITE FOR RESIDUE SO4 B 491
16BC7SOFTWARELYS B:444 , MET B:445BINDING SITE FOR RESIDUE SO4 B 492
17BC8SOFTWAREPHE B:420 , LYS B:427 , VAL B:453 , ALA B:454BINDING SITE FOR RESIDUE SO4 B 493
18BC9SOFTWARESER B:292 , ARG B:294 , GLN B:298 , LYS B:302BINDING SITE FOR RESIDUE SO4 B 494
19CC1SOFTWARETYR A:112 , ASN B:356 , VAL B:374 , ARG B:377BINDING SITE FOR RESIDUE SO4 B 495
20CC2SOFTWAREGLN B:432 , LYS B:435BINDING SITE FOR RESIDUE SO4 B 496
21CC3SOFTWAREVAL B:340 , TYR B:345 , ASN B:367BINDING SITE FOR RESIDUE SO4 B 497
22CC4SOFTWAREPHE A:354 , ASN B:91 , HOH B:590 , HOH B:648BINDING SITE FOR RESIDUE SO4 B 498
23CC5SOFTWAREPRO B:424 , GLY B:425 , GLU B:428 , HOH B:548BINDING SITE FOR RESIDUE SO4 B 499

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O08)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXOKINASE_2PS51748 Hexokinase domain profile.HXK_KLULA21-468
 		  2A:21-468
B:21-468
2HEXOKINASE_1PS00378 Hexokinase domain signature.HXK_KLULA152-177
 		  2A:152-177
B:152-177

(-) Exons   (0, 0)

(no "Exon" information available for 3O08)

(-) 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:471
 aligned with HXK_KLULA | P33284 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:471
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484 
            HXK_KLULA    15 SMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
               SCOP domains d3o08a1 A:15-223 automated matches                                                                                                                                                                               d3o08a2 A:224-485 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ee...........eeeeeeeee...eeeeeeeeee....eeeeeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhh.......eeeeee....ee.......ee...............hhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhhhhhh...........eeeee.hhhhh.........hhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhh...................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
                 3o08 A  15 SMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484 


Chain B from PDB  Type:PROTEIN  Length:479
 aligned with HXK_KLULA | P33284 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:479
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476         
            HXK_KLULA     7 KKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
               SCOP domains d3o08b1 B:7-223 automated matches                                                                                                                                                                                        d3o08b2 B:224-485 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Hexokinase_1-3o08B01 B:21-222                                                                                                                                                                             -Hexokinase_2-3o08B03 B:224-472                                                                                                                                                                                                                           ------------- Pfam domains (1)
           Pfam domains (2) --------------Hexokinase_1-3o08B02 B:21-222                                                                                                                                                                             -Hexokinase_2-3o08B04 B:224-472                                                                                                                                                                                                                           ------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........ee...........eeeeeeeee...eeeeeeeeee....eeeeeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhh.......eeeeeee...ee.......ee...............hhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhhhhhh...........eeeee.hhhhh.........hhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhh.hhhhhhhhhhhhhhh....hhhhh.eeeee.....hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------HEXOKINASE_2  PDB: B:21-468 UniProt: 21-468                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------HEXOKINASE_1              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o08 B   7 KKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O08)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  3o08
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  HXK_KLULA | P33284
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 Related Entries

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

UniProtKB/Swiss-Prot
        HXK_KLULA | P33284: 3o1b 3o1w 3o4w 3o5b 3o6w 3o80 3o8m 4jax

(-) Related Entries Specified in the PDB File

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)
3o8m CRYSTAL FORM XI OF KLHXK1 (MONONER) WITH GLUCOSE BOUND