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(-) Description

Title :  CRYSTAL STRUCTURE OF GALAKTOKINASE FROM PYROCOCCUS HORIKOSHII WITH AMP-PN AND GALACTOSE
 
Authors :  E. Inagaki, K. Sakamoto, A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Feb 06  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Galactokinase, Adp Analogue, Galactose, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Inagaki, K. Sakamoto, A. Shinkai, S. Yokoyama
Crystal Structure Of Galaktokinase From Pyrococcus Horikoshii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE GALACTOKINASE
    Chains: A
    EC Number: 2.7.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: GALACTOSE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1APW1Ligand/Ion{5'-O-[(R)-{[(S)-AMINO(HYDROXY-KAPPAO)PHOSPHORYL]OXY}(HYDROXY-KAPPAO)PHOSPHORYL]ADENOSINATO(2-)}MAGNESIUM
2GLA1Ligand/IonALPHA D-GALACTOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:9 , GLU A:15 , HIS A:16 , ASP A:18 , CYS A:145 , GLY A:146 , ASP A:149 , TYR A:198 , ALA A:303 , HOH A:1001 , HOH A:1003 , HOH A:1013 , HOH A:1105BINDING SITE FOR RESIDUE GLA A 401
2AC2SOFTWARESER A:47 , PHE A:50 , TRP A:67 , TYR A:70 , VAL A:92 , LEU A:98 , GLY A:99 , ALA A:100 , GLY A:101 , SER A:103 , SER A:104 , SER A:105 , PHE A:108 , ARG A:190 , HOH A:1005 , HOH A:1050 , HOH A:1061 , HOH A:1117 , HOH A:1194 , HOH A:1291 , HOH A:1326BINDING SITE FOR RESIDUE APW A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DEJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DEJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DEJ)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALACTOKINASEPS00106 Galactokinase signature.GAL1_PYRHO8-19  1A:8-19
2GHMP_KINASES_ATPPS00627 GHMP kinases putative ATP-binding domain.GAL1_PYRHO96-107  1A:96-107

(-) Exons   (0, 0)

(no "Exon" information available for 2DEJ)

(-) 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:346
 aligned with GAL1_PYRHO | O58107 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:350
                                    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
           GAL1_PYRHO     1 MIKVKSPGRVNLIGEHTDYTYGYVMPMAINLYTKIEAEKHGEVILYSEHFGEERKFSLNDLRKENSWIDYVKGIFWVLKESDYEVGGIKGRVSGNLPLGAGLSSSASFEVGILETLDKLYNLKLDSLSKVLLAKKAENEFVGVPCGILDQFAVVFGREGNVIFLDTHTLDYEYIPFPKDVSILVFYTGVRRELASSEYAERKHIAEESLKILGKGSSKEVREGELSKLPPLHRKFFGYIVRENARVLEVRDALKEGNVEEVGKILTTAHWDLAKNYEVSCKELDFFVERALKLGAYGARLTGAGFGGSAIALVDKEDAETIGEEILREYLKRFPWKARHFIVEPSDGVGI 350
               SCOP domains d2deja1 A:1-178 automated matches                                                                                                                                                 d2deja2 A:17    9-350 automated matches                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2dejA02 A:176-3    50  [code=3.30.70.890, no name defined]                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee...hhhhh.eeeeeeeeeeeeeeeeee..eeeee....eeeee..........hhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhh...eeeeee.....eeeee....eeeeeee....----hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...eeee.......eeeeeee..hhhhhhhhhhhhhhhhh....eeeee.ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GALACTOKINAS----------------------------------------------------------------------------GHMP_KINASES--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dej A   1 MIKVKSPGRVNLIGEHTDYTYGYVMPMAINLYTKIEAEKHGEVILYSEHFGEERKFSLNDLRKENSWIDYVKGIFWVLKESDYEVGGIKGRVSGNLPLGAGLSSSASFEVGILETLDKLYNLKLDSLSKVLLAKKAENEFVGVPCGILDQFAVVFGREGNVIFLDTHTLDYEYIPFPKDVSILVFYTGVR----SSEYAERKHIAEESLKILGKGSSKEVREGELSKLPPLHRKFFGYIVRENARVLEVRDALKEGNVEEVGKILTTAHWDLAKNYEVSCKELDFFVERALKLGAYGARLTGAGFGGSAIALVDKEDAETIGEEILREYLKRFPWKARHFIVEPSDGVGI 350
                                    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
                                                                                                                                                                                                                       190  195
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DEJ)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GAL1_PYRHO | O58107)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004335    galactokinase activity    Catalysis of the reaction: D-galactose + ATP = alpha-D-galactose 1-phosphate + ADP + 2 H(+).
    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: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:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
    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: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
        GAL1_PYRHO | O58107: 2cz9 2dei

(-) Related Entries Specified in the PDB File

2cz9 THE SAME PROTEIN
2dei THE SAME PROTEIN WITH AMP-PNP AND GALACTOSE RELATED ID: PHO001000369.3 RELATED DB: TARGETDB