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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM TRYPANOSOMA BRUCEI
 
Authors :  M. S. Alphey, D. C. Jones, A. H. Fairlamb
Date :  23 Jun 11  (Deposition) - 20 Jun 12  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Sleeping Sickness (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Jones, M. S. Alphey, S. Wyllie, A. H. Fairlamb
Chemical, Genetic And Structural Assessment Of Pyridoxal Kinase As A Drug Target In The African Trypanosome.
Mol. Microbiol. V. 86 51 2012
PubMed-ID: 22857512  |  Reference-DOI: 10.1111/J.1365-2958.2012.08189.X

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET3A
    Expression System Vector Type: PLASMID
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 185431
    Other Details: ATP APPEARS IN TWO ALTERNATE CONFORMATIONS
    Strain: TREU927
    Synonym: PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:242 , LYS A:250 , GLN A:289BINDING SITE FOR RESIDUE PO4 A 1300
2AC2SOFTWAREASP A:117 , ASN A:149 , GLU A:152 , LYS A:185 , SER A:186 , LEU A:196 , VAL A:217 , TYR A:219 , HIS A:220 , TYR A:224 , GLY A:226 , THR A:227 , GLY A:228 , MET A:252 , ILE A:259 , HOH A:2055BINDING SITE FOR RESIDUE ATP A 1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZS7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZS7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZS7)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZS7)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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   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:277
 aligned with O15927_9TRYP | O15927 from UniProtKB/TrEMBL  Length:300

    Alignment length:299
                                    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         
         O15927_9TRYP     1 MSEKTVLSIQSFVTHGYVGNKAATFPLQLHGFDVDGINTVCLSNHSGYPVIRGHRMSLQEYDELMEGVRANNFLSNYRYILTGYINNVDIIGRIRDTLKEVRELREKEDKKLTFICDPVMGDDGIMYCKKEVLDAYRELVPLADIVTPNYFEASLLSGVTVNDLSSAILAADWFHNCGVAHVIIKSFREQENPTHLRFLYSVKEGSEAAVRRFSGVVPYHEGRYTGTGDVFAACLLAFSHSHPMDVAIGKSMAVLQELIIATRKEGGDGKSSLKSRELRVVASPQVVLQPSTVVDVKPI 299
               SCOP domains d3zs7a_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhh....eeee....---------.hhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeee.---...eeeeeeee........eeeeeeee.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..----------........hhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zs7 A   1 MSEKTVLSIQSFVTHGYVGNKAATFPLQLHGFDVDGINTVCLSNHSGYPVIRGHRMSLQEYDELMEGVRANNFLSNYRYILTGYINNVDIIGRIRDTLKEVRELREKEDKKLTFICDPVM---------KEVLDAYRELVPLADIVTPNYFEASLLSGVTVNDLSSAILAADWFHNCGVAHVIIKSFR---NPTHLRFLYSVKEGSEAAVRRFSGVVPYHEGRYTGTGDVFAACLLAFSHSHPMDVAIGKSMAVLQELIIATRK----------SRELRVVASPQVVLQPSTVVDVKPI 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | - |     200       210       220       230       240       250       260   |     -    |  280       290         
                                                                                                                                                 120       130                                                       188 192                                                                     264        275
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZS7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZS7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (O15927_9TRYP | O15927)
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: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.
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.

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