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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM LACTOBACILLUS PLANTARUM IN COMPLEX WITH ADP
 
Authors :  A. Bagaria, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  22 Jun 09  (Deposition) - 30 Jun 09  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Pyridoxal Kinase, Adp, Psi-Ii, 11208C, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bagaria, D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Of Pyridoxal Kinase From Lactobacillus Plantarum In Complex With Adp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDX, LP_0863
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 1590
    Strain: WCFS1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:177 , ASP A:178 , ILE A:185 , LEU A:204 , GLY A:206 , THR A:211 , GLY A:212 , ASN A:237 , LEU A:240 , ASN A:241 , MG A:282 , HOH A:307 , HOH A:328 , HOH A:339 , HOH A:346 , HOH A:388 , HOH A:491 , HOH A:522BINDING SITE FOR RESIDUE ADP A 281
2AC2SOFTWAREADP A:281 , HOH A:307 , HOH A:318 , HOH A:346 , HOH A:382 , HOH A:446 , HOH A:522BINDING SITE FOR RESIDUE MG A 282

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HYO)

(-) 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:273
 aligned with F9UM74_LACPL | F9UM74 from UniProtKB/TrEMBL  Length:272

    Alignment length:273
                                                                                                                                                                                                                                                                                                         272 
                                    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 | 
         F9UM74_LACPL     1 MSTMLVAEDLSAVGGISLSSALPVLTAMQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAMRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNMAVAETIAQNRTDDRQGVALGDLLQAILALN-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...hhhhhhhhhhhh..eeeeeeeeeeee.........ee....hhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee....ee..ee....hhhhhhhhhhhhh...ee..hhhhhhhhhh.......hhhhhhhhhhh......ee.eeeeee..eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyo A   1 LSTmLVAEDLSAVGGISLSSALPVLTAmQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAmRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNmAVAETIAQNRTDDRQGVALGDLLQAILALNE 273
                               |    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   
                               |                      28-MSE                                                                                           126-MSE                                                                                                             242-MSE                           
                               4-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3HYO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (F9UM74_LACPL | F9UM74)
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.
    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.

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