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(-) Description

Title :  CRYSTAL STRUCTURE OF DIMERIC KLHXK1 IN CRYSTAL FORM IV
 
Authors :  E. B. Kuettner, K. Kettner, A. Keim, T. M. Kriegel, N. Strater
Date :  27 Jul 10  (Deposition) - 13 Oct 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
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  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NHE4Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3SO418Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:112 , GLU A:136 , HOH A:782 , ASN B:356 , VAL B:374 , ARG B:377 , SO4 B:496 , HOH B:732 , HOH B:889BINDING SITE FOR RESIDUE NHE A 486
02AC2SOFTWAREHIS A:117 , GLN A:125BINDING SITE FOR RESIDUE NHE A 487
03AC3SOFTWAREASN A:209 , ASP A:210 , THR A:211 , ILE A:230 , GLY A:234 , VAL A:235 , ASN A:236 , VAL B:2BINDING SITE FOR RESIDUE GOL A 488
04AC4SOFTWARETHR A:90 , ASN A:91 , LYS A:111 , ARG A:113 , HOH A:742BINDING SITE FOR RESIDUE SO4 A 489
05AC5SOFTWAREGLY A:232 , THR A:233 , GLY A:417 , SER A:418 , HOH A:635 , HOH A:749 , VAL B:2 , ARG B:3BINDING SITE FOR RESIDUE SO4 A 490
06AC6SOFTWAREGLU A:180 , GLY A:181 , HOH A:541 , HOH A:557BINDING SITE FOR RESIDUE SO4 A 491
07AC7SOFTWARESER A:292 , ARG A:294 , GLN A:298 , LYS A:302 , TYR A:308BINDING SITE FOR RESIDUE SO4 A 492
08AC8SOFTWAREGLN A:432 , LYS A:435 , HOH A:516BINDING SITE FOR RESIDUE SO4 A 493
09AC9SOFTWARELYS A:444 , MET A:445 , HOH A:593BINDING SITE FOR RESIDUE SO4 A 494
10BC1SOFTWARESER A:15 , MET A:16 , ALA A:17BINDING SITE FOR RESIDUE SO4 A 495
11BC2SOFTWAREPRO A:20 , ALA A:21 , HOH A:804BINDING SITE FOR RESIDUE SO4 A 496
12BC3SOFTWAREGLY A:417 , SER A:418 , ASN A:421 , ARG A:422 , ARG B:3BINDING SITE FOR RESIDUE SO4 A 497
13BC4SOFTWAREGLU A:39 , ARG A:42 , LYS A:46 , HOH A:663BINDING SITE FOR RESIDUE SO4 A 498
14BC5SOFTWARELYS A:40 , HIS A:276 , LEU A:277 , VAL A:278 , LEU A:279 , HOH A:890 , THR B:32 , LEU B:33 , LYS B:40 , HOH B:533 , HOH B:569 , HOH B:893BINDING SITE FOR RESIDUE NHE B 486
15BC6SOFTWAREASN A:356 , VAL A:374 , ARG A:377 , TYR B:112 , CYS B:133 , GLU B:136 , HOH B:631BINDING SITE FOR RESIDUE NHE B 487
16BC7SOFTWAREVAL A:2 , ASN B:209 , ASP B:210 , THR B:211 , GLY B:234 , ASN B:236 , HOH B:683 , HOH B:775BINDING SITE FOR RESIDUE GOL B 488
17BC8SOFTWAREVAL A:2 , GLY B:232 , THR B:233 , GLY B:417 , SER B:418 , HOH B:794BINDING SITE FOR RESIDUE SO4 B 489
18BC9SOFTWAREGLN B:432 , LYS B:435BINDING SITE FOR RESIDUE SO4 B 490
19CC1SOFTWARESER B:292 , ARG B:294 , GLN B:298 , LYS B:302 , TYR B:308BINDING SITE FOR RESIDUE SO4 B 491
20CC2SOFTWAREPHE B:420 , LYS B:427 , VAL B:453 , ALA B:454 , HOH B:518BINDING SITE FOR RESIDUE SO4 B 492
21CC3SOFTWARETHR B:90 , ASN B:91 , LYS B:111 , ARG B:113BINDING SITE FOR RESIDUE SO4 B 493
22CC4SOFTWARELYS A:283 , HIS B:276 , ARG B:281 , VAL B:286 , HOH B:564 , HOH B:680 , HOH B:793 , HOH B:873BINDING SITE FOR RESIDUE SO4 B 494
23CC5SOFTWAREPRO B:20 , ALA B:21 , HOH B:531BINDING SITE FOR RESIDUE SO4 B 495
24CC6SOFTWARENHE A:486 , HOH A:790 , THR B:373 , VAL B:374 , HOH B:559 , HOH B:732BINDING SITE FOR RESIDUE SO4 B 496

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O4W)

(-) 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 3O4W)

(-) 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:484
 aligned with HXK_KLULA | P33284 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:484
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481    
            HXK_KLULA     2 VRLGPKKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
               SCOP domains d3o4wa1 A:2-223 automated matches                                                                                                                                                                                             d3o4wa2 A:224-485 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ee...........eeeeeeeee...eeeeeeeeee....eeeeeeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeeee....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
                 3o4w A   2 VRLGPKKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481    


Chain B from PDB  Type:PROTEIN  Length:484
 aligned with HXK_KLULA | P33284 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:484
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481    
            HXK_KLULA     2 VRLGPKKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
               SCOP domains d3o4wb1 B:2-223 automated matches                                                                                                                                                                                             d3o4wb2 B:224-485 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Hexokinase_1-3o4wB01 B:21-222                                                                                                                                                                             -Hexokinase_2-3o4wB03 B:224-472                                                                                                                                                                                                                           ------------- Pfam domains (1)
           Pfam domains (2) -------------------Hexokinase_1-3o4wB02 B:21-222                                                                                                                                                                             -Hexokinase_2-3o4wB04 B:224-472                                                                                                                                                                                                                           ------------- Pfam domains (2)
         Sec.struct. author ..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........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
                 3o4w B   2 VRLGPKKPPARKGSMADVPANLMEQIHGLETLFTVSSEKMRSIVKHFISELDKGLSKKGGNIPMIPGWVVEYPTGKETGDFLALDLGGTNLRVVLVKLGGNHDFDTTQNKYRLPDHLRTGTSEQLWSFIAKCLKEFVDEWYPDGVSEPLPLGFTFSYPASQKKINSGVLQRWTKGFDIEGVEGHDVVPMLQEQIEKLNIPINVVALINDTTGTLVASLYTDPQTKMGIIIGTGVNGAYYDVVSGIEKLEGLLPEDIGPDSPMAINCEYGSFDNEHLVLPRTKYDVIIDEESPRPGQQAFEKMTSGYYLGEIMRLVLLDLYDSGFIFKDQDISKLKEAYVMDTSYPSKIEDDPFENLEDTDDLFKTNLNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICDKRGYKTAHIAADGSVFNRYPGYKEKAAQALKDIYNWDVEKMEDHPIQLVAAEDGSGVGAAIIACLTQKRLAAGKSVGIKGE 485
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 3O4W)

(-) 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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  HXK_KLULA | P33284
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 Related Entries

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

UniProtKB/Swiss-Prot
        HXK_KLULA | P33284: 3o08 3o1b 3o1w 3o5b 3o6w 3o80 3o8m 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)
3o5b CRYSTAL FORM VII OF KLHXK1 (DIMER) WITH GLUCOSE BOUND
3o6w CRYSTAL FORM VIII OF KLHXK1 (MONOMER)
3o80 CRYSTAL FORM IX OF KLHXK1 (MONOMER)
3o8m CRYSTAL FORM XI OF KLHXK1 (MONONER) WITH GLUCOSE BOUND