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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ADP-DEPENDENT GLUCOKINASE FROM PYROCOCCUS FURIOSUS
 
Authors :  S. Ito, J. J. Jeong, I. Yoshioka, S. Koga, S. Fushinobu, H. Shoun, T. Wakagi
Date :  27 Feb 03  (Deposition) - 27 Feb 04  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ito, S. Fushinobu, J. J. Jeong, I. Yoshioka, S. Koga, H. Shoun, T. Wakagi
Crystal Structure Of An Adp-Dependent Glucokinase From Pyrococcus Furiosus: Implications For A Sugar-Induced Conformational Change In Adp-Dependent Kinase
J. Mol. Biol. V. 331 871 2003
PubMed-ID: 12909015  |  Reference-DOI: 10.1016/S0022-2836(03)00792-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-DEPENDENT GLUCOKINASE
    Chains: A
    EC Number: 2.7.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: GLUCOKINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2BGC1Ligand/IonBETA-D-GLUCOSE
3GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:30 , ASN A:32 , ASP A:34 , GLU A:88 , GLY A:111 , GLY A:112 , GLN A:113 , ILE A:116 , HIS A:176 , ASP A:440 , HOH A:1487 , HOH A:1575 , HOH A:1616 , HOH A:1790BINDING SITE FOR RESIDUE GLC A 1457
2AC2SOFTWAREASN A:32 , ASP A:34 , GLU A:88 , GLY A:111 , GLY A:112 , GLN A:113 , ILE A:116 , HIS A:176 , ASP A:440 , HOH A:1487 , HOH A:1616 , HOH A:1790 , HOH A:1953BINDING SITE FOR RESIDUE BGC A 2457
3AC3SOFTWAREGLU A:195 , ASN A:292 , HIS A:342 , THR A:343 , TYR A:344 , TYR A:347 , LYS A:427 , ILE A:428 , VAL A:429 , PRO A:432 , ILE A:438 , GLY A:439 , ILE A:442 , HOH A:1460 , HOH A:1464 , HOH A:1466 , HOH A:1470 , HOH A:1561 , HOH A:1658 , HOH A:1683 , HOH A:1780BINDING SITE FOR RESIDUE AMP A 1456

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UA4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:28 -Tyr A:29
2Asp A:316 -Pro A:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UA4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.GLKA_PYRFU2-455  1A:2-455

(-) Exons   (0, 0)

(no "Exon" information available for 1UA4)

(-) 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:454
 aligned with GLKA_PYRFU | Q9V2Z6 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:454
                                    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    
           GLKA_PYRFU     2 PTWEELYKNAIEKAIKSVPKVKGVLLGYNTNIDAIKYLDSKDLEERIIKAGKEEVIKYSEELPDKINTVSQLLGSILWSIRRGKAAELFVESCPVRFYMKRWGWNELRMGGQAGIMANLLGGVYGVPVIVHVPQLSRLQANLFLDGPIYVPTLENGEVKLIHPKEFSGDEENCIHYIYEFPRGFRVFEFEAPRENRFIGSADDYNTTLFIREEFRESFSEVIKNVQLAILSGLQALTKENYKEPFEIVKSNLEVLNEREIPVHLEFAFTPDEKVREEILNVLGMFYSVGLNEVELASIMEILGEKKLAKELLAHDPVDPIAVTEAMLKLAKKTGVKRIHFHTYGYYLALTEYKGEHVRDALLFAALAAAAKAMKGNITSLEEIREATSVPVNEKATQVEEKLRAEYGIKEGIGEVEGYQIAFIPTKIVAKPKSTVGIGDTISSSAFIGEFSFTL 455
               SCOP domains d1ua4a_ A: ADP-dependent glucokinase                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ua4A01                       1ua4A02 A:32-111,A:173-204  [code=3.30.1110.20, no name defined]                1ua4A01 A:2-31,A:112-172,A:205-455                           1ua4A02 A:32-111,A:173-204      1ua4A01 A:2-31,A:112-172,A:205-455  [code=3.40.1190.20, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ----------------ADP_PFK_GK-1ua4A01 A:18-451                                                                                                                                                                                                                                                                                                                                                                                                                       ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..eeeeehhhhhhhhhhh......eee.....hhhhhh......eeeeeee..eeeeehhhhh.......eeeeeee....ee..ee....eeeeee...hhhhh..hhhhh.hhhhhhhhh.eeee.hhhhh....hhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee...eeeeee...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhh....eeee..eeeeeee...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ADPK  PDB: A:2-455 UniProt: 2-455                                                                                                                                                                                                                                                                                                                                                                                                                                      PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ua4 A   2 PTWEELYKNAIEKAIKSVPKVKGVLLGYNTNIDAIKYLDSKDLEERIIKAGKEEVIKYSEELPDKINTVSQLLGSILWSIRRGKAAELFVESCPVRFYMKRWGWNELRMGGQAGIMANLLGGVYGVPVIVHVPQLSRLQANLFLDGPIYVPTLENGEVKLIHPKEFSGDEENCIHYIYEFPRGFRVFEFEAPRENRFIGSADDYNTTLFIREEFRESFSEVIKNVQLAILSGLQALTKENYKEPFEIVKSNLEVLNEREIPVHLEFAFTPDEKVREEILNVLGMFYSVGLNEVELASIMEILGEKKLAKELLAHDPVDPIAVTEAMLKLAKKTGVKRIHFHTYGYYLALTEYKGEHVRDALLFAALAAAAKAMKGNITSLEEIREATSVPVNEKATQVEEKLRAEYGIKEGIGEVEGYQIAFIPTKIVAKPKSTVGIGDTISSSAFIGEFSFTL 455
                                    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
   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  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLKA_PYRFU | Q9V2Z6)
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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