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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-PYRIDOXOLACTONASE, 5-PYRIDOXOLACTONE BOUND
 
Authors :  J. Kobayashi, Y. Yoshikane, S. Baba, K. Mizutani, N. Takahashi, B. Mika
Date :  26 Apr 13  (Deposition) - 09 Apr 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha-Beta/Beta-Alpha Fold, Hydrolase, Lactone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kobayashi, Y. Yoshikane, T. Yagi, S. Baba, K. Mizutani, N. Takahashi, B. Mikami
Structure Of 4-Pyridoxolactonase From Mesorhizobium Loti
Acta Crystallogr. , Sect. F V. 70 424 2014
PubMed: search  |  Reference-DOI: 10.1107/S2053230X14003926

(-) Compounds

Molecule 1 - 4-PYRIDOXOLACTONASE
    Chains: A
    EC Number: 3.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MLR6805
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
15PN2Ligand/Ion7-HYDROXY-6-METHYLFURO[3,4-C]PYRIDIN-3(1H)-ONE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
15PN4Ligand/Ion7-HYDROXY-6-METHYLFURO[3,4-C]PYRIDIN-3(1H)-ONE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3GOL6Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
15PN4Ligand/Ion7-HYDROXY-6-METHYLFURO[3,4-C]PYRIDIN-3(1H)-ONE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3GOL6Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:100 , HIS A:101 , ASP A:207 , HIS A:252 , HOH A:401BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:96 , HIS A:98 , HIS A:185 , ASP A:207 , HOH A:401BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREGLU A:65 , HIS A:98 , PHE A:99 , LEU A:132 , GLY A:133 , TYR A:210 , PHE A:223 , HOH A:401BINDING SITE FOR RESIDUE 5PN A 303
04AC4SOFTWAREASP A:10 , SER A:13 , ILE A:68 , GLU A:70 , GLN A:73 , MET A:254 , LYS A:258BINDING SITE FOR RESIDUE 5PN A 304
05AC5SOFTWARECYS A:115 , HIS A:116 , ARG A:117 , VAL A:120 , GLY A:166BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREGLU A:142 , ARG A:159 , ARG A:199 , ARG A:261 , GLY A:268 , HIS A:269 , HIS A:271BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREVAL A:31 , ARG A:32 , PHE A:33 , THR A:211 , HIS A:252 , ASP A:253 , MET A:254BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWAREASP A:54 , LYS A:106 , ASP A:136 , SER A:138BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREARG A:32 , MET A:254BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREASN A:125 , PRO A:126 , GLN A:127 , PRO A:128BINDING SITE FOR RESIDUE EDO A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KEQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KEQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KEQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4KEQ)

(-) 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:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhh.......eeeeeeeeeeeee..eeeee....hhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhh.eee....hhhhh.hhhhh...eeeee.hhhhhhhh..............hhhhhhhh.hhhhh.....hhhh.eeee...eeee..eeeee........eeeee.......eee.hhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eee...hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4keq A   3 DTKVYLLDGGSLVLDGYHVFWNRGPGGEVRFPVYSILIEHAEGRFLIDTGYDYDHVMKVLPFEKPIQEKHQTIPGALGLLGLEPRDIDVVVNSHFHFDHCGGNKYFPHAKKICHRSEVPQACNPQPFEHLGYSDLSFSAEAAEARGATAQLLEGTTRANSTFEGIDGDVDLARGVKLISTPGHSIGHYSLLVEFPRRKPILFTIDAAYTQKSLETLCQAAFHIDPVAGVNSMRKVKKLAEDHGAELMYSHDMDNFKTYRTGTQFYGHHHH 272
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   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 4KEQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KEQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KEQ)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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    Gly A:26 - Pro A:27   [ RasMol ]  
 
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 Related Entries

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        PDLA_RHILO | Q988B9: 3aj3 4kep

(-) Related Entries Specified in the PDB File

3aj3 SELENOMETHIONINE SUBSTITUTED
4kep WILD-TYPE