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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM LACTOBACILLUS PLANTARUM
 
Authors :  A. Bagaria, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Re Center For Structural Genomics (Nysgxrc)
Date :  24 Apr 09  (Deposition) - 26 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Pyridoxal Kinase, 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
To Be Published
PubMed: search

(-) 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:139 , GLY A:212 , HOH A:328 , HOH A:342 , HOH A:351 , HOH A:361 , HOH A:375 , HOH A:405 , HOH A:436 , HOH A:502 , HOH A:523BINDING SITE FOR RESIDUE SO4 A 281
2AC2SOFTWARESER A:0 , GLN A:250 , ARG A:252 , ALA A:260 , LEU A:261 , GLY A:262 , HOH A:349 , HOH A:385 , HOH A:442 , HOH A:538BINDING SITE FOR RESIDUE SO4 A 282
3AC3SOFTWAREARG A:203 , LEU A:204 , ASN A:241 , HOH A:447 , HOH A:546 , HOH A:557BINDING SITE FOR RESIDUE GOL A 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H74)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H74)

(-) Exons   (0, 0)

(no "Exon" information available for 3H74)

(-) 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:278
 aligned with F9UM74_LACPL | F9UM74 from UniProtKB/TrEMBL  Length:272

    Alignment length:278
                             1                                                                                                                                                                                                                                                                            272     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  |     
         F9UM74_LACPL     - -MSTMLVAEDLSAVGGISLSSALPVLTAMQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAMRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNMAVAETIAQNRTDDRQGVALGDLLQAILALN-----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhhhhhhhhh.eeeeeeeeeeeee.........ee....hhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh...eeee....ee..ee....hhhhhhhhhhhhhhh.ee..hhhhhhhhhh.......hhhhhhhhhhh......ee.eeeeee..eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h74 A   0 SLSTmLVAEDLSAVGGISLSSALPVLTAmQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAmRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNmAVAETIAQNRTDDRQGVALGDLLQAILALNEHHHH 280
                                |    9        19        29        39        49        59        69        79        89        99       109       119      |129       139       149       159       169       179       189       199       209       219       229       239  |    249       259       269   ||   
                                |                      28-MSE                                                                                           126-MSE                                                                                                             242-MSE                        273|   
                                4-MSE                                                                                                                                                                                                                                                                       277
   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  (0, 0)

(no "SCOP Domain" information available for 3H74)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H74)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H74)

(-) 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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 Related Entries

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        F9UM74_LACPL | F9UM74: 3hyo 3ibq

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