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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAL KINASE IN COMPLEX WITH ROSCOVITINE AND DERIVATIVES
 
Authors :  L. Tang, M. -H. Li, P. Cao, F. Wang, W. -R. Chang, S. Bach, J. Reinhardt, Y. Ferandin, M. Koken, H. Galons, Y. Wan, N. Gray, L. Meijer, T. Jiang, D. -C. Liang
Date :  09 Jan 05  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Structure, Complexed With O6-(R)-Roscovitine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tang, M. -H. Li, P. Cao, F. Wang, W. -R. Chang, S. Bach, J. Reinhardt, Y. Ferandin, H. Galons, Y. Wan, N. Gray, L. Meijer, T. Jiang, D. -C. Liang
Crystal Structure Of Pyridoxal Kinase In Complex With Roscovitine And Derivatives.
J. Biol. Chem. V. 280 31220 2005
PubMed-ID: 15985434  |  Reference-DOI: 10.1074/JBC.M500805200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A
    EC Number: 2.7.1.35
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
    Synonym: PYRIDOXINE KINASE

 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
1R6C1Ligand/Ion(2R)-2-{[6-(BENZYLOXY)-9-ISOPROPYL-9H-PURIN-2-YL]AMINO}BUTAN-1-OL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:12 , VAL A:19 , PHE A:43 , HIS A:46 , THR A:47 , TYR A:84 , ARG A:86 , ASP A:235BINDING SITE FOR RESIDUE R6C A 313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1YHJ)

(-) 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:307
 aligned with PDXK_SHEEP | P82197 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:307
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       
           PDXK_SHEEP     6 RVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDELQELYDGLKLNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREKVVPVADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRAPDGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 312
               SCOP domains d1yhja_ A: Pyridoxal kinase                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1yhjA00 A:6-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                               CATH domains
               Pfam domains PfkB-1yhjA01 A:6-284                                                                                                                                                                                                                                                                   ---------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...eeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeee............eeeeeeee...........eeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yhj A   6 RVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDELQELYDGLKLNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREKVVPVADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRAPDGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDXK_SHEEP | P82197)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0008478    pyridoxal kinase activity    Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
    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: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.
    GO:0009443    pyridoxal 5'-phosphate salvage    Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
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
        PDXK_SHEEP | P82197: 1lhp 1lhr 1rft 1rfu 1rfv 1ygj 1ygk

(-) Related Entries Specified in the PDB File

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