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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)
 
Authors :  A. Herrera-Morande, J. A. Rivas-Pardo, F. J. Fernandez, V. Guixe, M. C.
Date :  30 Aug 12  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Ribokinase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Rivas-Pardo, A. Herrera-Morande, V. Castro-Fernandez, F. J. Fernandez, M. C. Vega, V. Guixe
Crystal Structure, Saxs And Kinetic Mechanism Of Hyperthermophilic Adp-Dependent Glucokinase From Thermococcus Litoralis Reveal A Conserved Mechanism For Catalysis.
Plos One V. 8 66687 2013
PubMed-ID: 23818958  |  Reference-DOI: 10.1371/JOURNAL.PONE.0066687

(-) Compounds

Molecule 1 - ADP-DEPENDENT GLUCOKINASE
    Chains: A
    EC Number: 2.7.1.147
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET-17B
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS LITORALIS
    Organism Taxid: 2265
    Synonym: ADP-GK, ADPGK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:38 , ASP A:42 , GLU A:96 , GLY A:119 , GLY A:120 , ILE A:124 , HIS A:184 , VAL A:447 , ASP A:451 , HOH A:2152 , HOH A:2160BINDING SITE FOR RESIDUE GLC A 468
2AC2SOFTWAREGLU A:279 , GLY A:303 , LEU A:304 , ASN A:305 , GLU A:308 , HIS A:352 , AMP A:1472 , HOH A:2040 , HOH A:2096 , HOH A:2154BINDING SITE FOR RESIDUE GOL A1468
3AC3SOFTWARELYS A:275 , THR A:300 , TYR A:363 , GLU A:461 , PHE A:462 , ARG A:465BINDING SITE FOR RESIDUE GOL A1469
4AC4SOFTWAREASN A:22 , ASP A:370 , MET A:464 , HOH A:2128 , HOH A:2155 , HOH A:2161BINDING SITE FOR RESIDUE GOL A1470
5AC5SOFTWAREPRO A:142 , TYR A:218 , MET A:219 , GLU A:412BINDING SITE FOR RESIDUE GOL A1471
6AC6SOFTWAREGLU A:203 , ASN A:305 , HIS A:352 , THR A:353 , LYS A:438 , VAL A:440 , ILE A:449 , ILE A:453 , GOL A:1468 , HOH A:2122 , HOH A:2153 , HOH A:2162BINDING SITE FOR RESIDUE AMP A1472
7AC7SOFTWAREASP A:318 , GLU A:319 , GLU A:320 , LEU A:321BINDING SITE FOR RESIDUE GOL A1473

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B8S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:36 -Tyr A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B8S)

(-) 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 4B8S)

(-) 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:466
 aligned with GLKA_THELN | Q7M537 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:466
                                    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      
           GLKA_THELN     2 KESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDKDDLEKRVTEIGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYRDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
               SCOP domains d4b8sa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeeeehhhhhhhhhhhhh....eee.....hhhhhh......eeeeeee..eeeeehhhhh.......eeeeeee....ee..ee....eeeeeee..hhhhh..hhhhhhhhhhhhh...eeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee...eeeeee....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhh......eee....eeeeee...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ADPK  PDB: A:10-467 UniProt: 10-467                                                                                                                                                                                                                                                                                                                                                                                                                                        PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b8s A   2 KESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDKDDLEKRVTEIGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYRDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
                                    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
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B8S)

(-) 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: 1gc5 4b8r

(-) Related Entries Specified in the PDB File

4b8r CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)