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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS
 
Authors :  S. Ito, S. Fushinobu, I. Yoshioka, S. Koga, H. Matsuzawa, T. Wakagi
Date :  20 Jul 00  (Deposition) - 25 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alfa/Beta Sandwichs, Induced-Fitting, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ito, S. Fushinobu, I. Yoshioka, S. Koga, H. Matsuzawa, T. Wakagi
Structural Basis For The Adp-Specificity Of A Novel Glucokinase From A Hyperthermophilic Archaeon
Structure V. 9 205 2001
PubMed-ID: 11286887  |  Reference-DOI: 10.1016/S0969-2126(01)00577-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-DEPENDENT GLUCOKINASE
    Chains: A
    EC Number: 2.7.1.147
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS LITORALIS
    Organism Taxid: 2265

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:305 , HIS A:352 , THR A:353 , LYS A:438 , VAL A:440 , PRO A:443 , ILE A:449 , GLY A:450 , ILE A:453 , HOH A:555BINDING SITE FOR RESIDUE ADP A 470

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GC5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.GLKA_THELN10-467  1A:10-467

(-) Exons   (0, 0)

(no "Exon" information available for 1GC5)

(-) 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:467
 aligned with GLKA_THELN | Q7M537 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:467
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       
           GLKA_THELN     1 MKESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDKDDLEKRVTEIGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYRDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
               SCOP domains d1gc5a_ A: ADP-dependent glucokinase                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1gc5A01 A:1-40,A:119-181,A:211-467      1gc5A02 A:41-118,A:182-209  [code=3.30.1110.20, no name defined]              1gc5A01 A:1-40,A:119-181,A:211-467                             1gc5A02 A:41-118,A:182-209  -1gc5A01 A:1-40,A:119-181,A:211-467  [code=3.40.1190.20, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeeeehhhhhhhhhhhhh....eee.....hhhhhh......eeeeee....eeeehhhhh.......eeeeeee....ee..ee....eeeeee..........hhhhhhhhhhhhh...eeee.hhhhh........hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhheeee..eee....eeeeee...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ADPK  PDB: A:10-467 UniProt: 10-467                                                                                                                                                                                                                                                                                                                                                                                                                                        PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gc5 A   1 MKESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDADDLEKRVTEKGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYKDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GC5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLKA_THELN | Q7M537)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        GLKA_THELN | Q7M537: 4b8r 4b8s

(-) Related Entries Specified in the PDB File

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