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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM LACTOBACILLUS PLANTARUM IN COMPLEX WITH ATP
 
Authors :  A. Bagaria, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  16 Jul 09  (Deposition) - 28 Jul 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Pyridoxal Kinase, Atp, 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 Atp
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 Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:177 , ASP A:178 , LEU A:204 , TYR A:208 , THR A:211 , GLY A:212 , ASN A:237 , LEU A:240 , ASN A:241 , MG A:282 , HOH A:340 , HOH A:353 , HOH A:358 , HOH A:359 , HOH A:447BINDING SITE FOR RESIDUE ATP A 281
2AC2SOFTWAREATP A:281 , HOH A:348 , HOH A:358 , HOH A:427 , HOH A:447 , HOH A:448BINDING SITE FOR RESIDUE MG A 282

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IBQ)

(-) Sequences/Alignments

Asymmetric 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:272
 aligned with F9UM74_LACPL | F9UM74 from UniProtKB/TrEMBL  Length:272

    Alignment length:272
                                                                                                                                                                                                                                                                                                        272 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271| 
         F9UM74_LACPL     2 STMLVAEDLSAVGGISLSSALPVLTAMQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAMRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNMAVAETIAQNRTDDRQGVALGDLLQAILALN-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhh..eeeeeeeeeeee.........ee...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh...eeee....ee..ee....hhhhhhhhhhhhh...ee..hhhhhhhhhh.......hhhhhhhhhhh......ee.eeeeee..eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ibq A   2 STmLVAEDLSAVGGISLSSALPVLTAmQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAmRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNmAVAETIAQNRTDDRQGVALGDLLQAILALNE 273
                              |     11        21      | 31        41        51        61        71        81        91       101       111       121    |  131       141       151       161       171       181       191       201       211       221       231       241|      251       261       271  
                              |                      28-MSE                                                                                           126-MSE                                                                                                             242-MSE                           
                              4-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3IBQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric 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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