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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS GALACTOKINASE COMPLEXED WITH GALACTOSE
 
Authors :  J. B. Thoden, H. M. Holden
Date :  30 May 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Galactose, Galactosemia, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, H. M. Holden
Molecular Structure Of Galactokinase
J. Biol. Chem. V. 278 33305 2003
PubMed-ID: 12796487  |  Reference-DOI: 10.1074/JBC.M304789200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALACTOKINASE
    Chains: A
    EC Number: 2.7.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GALK
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    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
1GLA1Ligand/IonALPHA D-GALACTOSE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , GLU A:42 , HIS A:43 , ASP A:45 , TYR A:46 , SER A:179 , GLY A:180 , ASP A:183 , TYR A:233 , ALA A:348 , PO4 A:401 , HOH A:406 , HOH A:478BINDING SITE FOR RESIDUE GLA A 400
2AC2SOFTWAREARG A:36 , GLY A:135 , LEU A:136 , SER A:137 , ASP A:183 , ALA A:348 , GLA A:400 , HOH A:403BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALACTOKINASEPS00106 Galactokinase signature.GAL1_LACLA35-46  1A:35-46
2GHMP_KINASES_ATPPS00627 GHMP kinases putative ATP-binding domain.GAL1_LACLA130-141  1A:130-141

(-) Exons   (0, 0)

(no "Exon" information available for 1PIE)

(-) 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:388
 aligned with GAL1_LACLA | Q9R7D7 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:388
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
           GAL1_LACLA     9 TVLSALTEKFAEVFGDTKEVEYFFSPGRINLIGEHTDYNGGYVFPASITIGTTGLARLREDKKVKLYSENFPKLGVIEFDLDEVEKKDGELWSNYVKGMIVMLKGAGYEIDKGFELLIKGEIPTASGLSSSASLELLVGVVLDDLFNLNVPRLELVQLGQKTENDYIGVNSGILDQFAIGFGEVKKAILLDCNTLKYEMVPVELRDYDIVIMNTNKPRALTESKYNERFAETREALKRMQTRLDIQSLGELSNEEFDANTDLIGDETLIKRARHAVYENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARMTGAGFGGCAIALVAHDNVSAFEKAVGQVYEEVVGYPASFYVAQIGSGSTKL 396
               SCOP domains d1piea1 A:9-213 Galactokinase                                                                                                                                                                                d1piea2 A:214-396 Galactokinase                                                                                                                                                         SCOP domains
               CATH domains 1pieA01 A:9-209,A:387-396  [code=3.30.230.10, no name defined]                                                                                                                                           1pieA02 A:210-386  [code=3.30.70.890, no name defined]                                                                                                                           1pieA01    CATH domains
               Pfam domains ------GalKase_gal_bdg-1pieA03 A:15-67                      -------------------------------------------------------GHMP_kinases_N-1pieA01 A:123-191                                     -----------------------------------------------------------------------------------------------------GHMP_kinases_C-1pieA02 A:293-376                                                    -------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.....eeeeeeeeeeee.........eeeeeeeeeeeeeeeee....eeeeee..hhhhh.eeee...........hhhhhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhh...eeeeee.....eeeee.....eeeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeeeee.......eeeeeee..hhhhhhhhhhhhhhhhhh...eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GALACTOKINAS-----------------------------------------------------------------------------------GHMP_KINASES--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pie A   9 TVLSALTEKFAEVFGDTKEVEYFFSPGRINLIGEHTDYNGGYVFPASITIGTTGLARLREDKKVKLYSENFPKLGVIEFDLDEVEKKDGELWSNYVKGMIVMLKGAGYEIDKGFELLIKGEIPTASGLSSSASLELLVGVVLDDLFNLNVPRLELVQLGQKTENDYIGVNSGILDQFAIGFGEVKKAIELDCNTLKYEMVPVELRDYDIVIMNTNKPRALTESKYNERFAETREALKRMQTRLDIQSLGELSNEEFDANTDLIGDETLIKRARHAVYENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARMTGAGFGGCAIALVAHDNVSAFRKAVGQVYEEVVGYPASFYVAQIGSGSTKL 396
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: GHMP_kinases_C] (13)
(-)
Clan: no clan defined [family: GalKase_gal_bdg] (3)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GAL1_LACLA | Q9R7D7)
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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