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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP-DEPENDENT GLUCOKINASE FROM A PYROCOCCUS HORIKOSHII
 
Authors :  H. Tsuge, H. Sakuraba, N. Katunuma, T. Ohshima
Date :  22 Feb 02  (Deposition) - 30 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Adp Glucokinase Apo, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tsuge, H. Sakuraba, T. Kobe, A. Kujime, N. Katunuma, T. Ohshima
Crystal Structure Of The Adp-Dependent Glucokinase From Pyrococcus Horikoshii At 2. 0-A Resolution: A Large Conformational Change In Adp-Dependent Glucokinase
Protein Sci. V. 11 2456 2002
PubMed-ID: 12237466  |  Reference-DOI: 10.1110/PS.0215602
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-DEPENDENT GLUCOKINASE
    ChainsA
    EC Number2.7.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid53953

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1L2L)

(-) Sites  (0, 0)

(no "Site" information available for 1L2L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L2L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L2L)

(-) Exons   (0, 0)

(no "Exon" information available for 1L2L)

(-) 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:432
 aligned with GLKA_PYRHO | O58328 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:451
                                    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 
           GLKA_PYRHO     7 WESLYEKALDKVEASIRKVRGVLLAYNTNIDAIKYLKREDLEKRIEKVGKEEVLRYSEELPKEIETIPQLLGSILWSIKRGKAAELLVVSREVREYMRKWGWDELRMGGQVGIMANLLGGVYGIPVIAHVPQLSELQASLFLDGPIYVPTFERGELRLIHPREFRKGEEDCIHYIYEFPRNFKVLDFEAPRENRFIGAADDYNPILYVREEWIERFEEIAKRSELAIISGLHPLTQENHGKPIKLVREHLKILNDLGIRAHLEFAFTPDEVVRLEIVKLLKHFYSVGLNEVELASVVSVMGEKELAERIISKDPADPIAVIEGLLKLIKETGVKRIHFHTYGYYLALTREKGEHVRDALLFSALAAATKAMKGNIEKLSDIREGLAVPIGEQGLEVEKILEKEFSLRDGIGSIEDYQLTFIPTKVVKKPKSTVGIGDTISSSAFVSEFSLH 457
               SCOP domains d1l2la_ A: ADP-dependent glucokinase                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1l2lA01                      1l2lA02 A:36-113,A:177-204  [code=3.30.1110.20, no name defined]              1l2lA01 A:7-35,A:114-176,A:206-454                             1l2lA02 A:36-113,A:177-204  -1l2lA01 A:7-35,A:114-176,A:206-454  [code=3.40.1190.20, no name defined]                                                                                                                                                                                 --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..eeeeehhhhhhhhhhh......eee.....hhhhhhh.....ee...------...hhhhh----...eee..ee....ee..ee....eeeeeee..hhhhh..hhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeee..eeeeeee..---------..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2l A   7 WESLYEKALDKVEASIRKVRGVLLAYNTNIDAIKYLKREDLEKRIEKVGKEEVLRYSEELPKEIETIPQLLGSILWSIKRGKAAELLVVSREVREYMRKWGWDELRMGGQVGIMANLLGGVYGIPVIAHVPQLSELQASLFLDGPIYVPT------RLIHPREF----EDCIHYIYEFPRNFKVLDFEAPRENRFIGAADDYNPILYVREEWIERFEEIAKRSELAIISGLHPLTQENHGKPIKLVREHLKILNDLGIRAHLEFAFTPDEVVRLEIVKLLKHFYSVGLNEVELASVVSVMGEKELAERIISKDPADPIAVIEGLLKLIKETGVKRIHFHTYGYYLALTREKGEHVRDALLFSALAAATKAMKGNIEKLSDIREGLAVPIGEQGLEVEKILEKEFSLRDGIGSIEDYQLTFIPTK---------GIGDTISSSAFVSEFSLH 457
                                    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   |     -   |   446       456 
                                                                                                                                                                               156    163    170  175                                                                                                                                                                                                                                                            430       440                 

   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L2L)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLKA_PYRHO | O58328)
molecular function
    GO:0043843    ADP-specific glucokinase activity    Catalysis of the reaction: ADP + D-glucose = AMP + D-glucose 6-phosphate.
    GO:0004340    glucokinase activity    Catalysis of the reaction: ATP + D-glucose = ADP + D-glucose-6-phosphate.
    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: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:0051156    glucose 6-phosphate metabolic process    The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Asp A:319 - Pro A:320   [ RasMol ]  
 

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