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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOMETHIONINE SUBSTITUTED 4-PYRIDOXOLACTONASE FROM MESORHIZOBIUM LOTI
 
Authors :  J. Kobayashi, Y. Yoshikane, S. Baba, B. Mikami, T. Yagi
Date :  21 May 10  (Deposition) - 25 May 11  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Zn-Protein, Metallo-Beta-Lactamase, Hydrolase (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: 381
    Strain: MAFF303099
    Synonym: MLR6805 PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:100 , HIS A:101 , ASP A:207 , HIS A:252 , ZN A:276 , HOH A:384 , HOH A:502BINDING SITE FOR RESIDUE ZN A 275
2AC2SOFTWAREHIS A:96 , HIS A:98 , HIS A:185 , ASP A:207 , ZN A:275 , HOH A:420 , HOH A:502BINDING SITE FOR RESIDUE ZN A 276
3AC3SOFTWAREARG A:199 , ARG A:261 , TYR A:267 , GLY A:268 , HIS A:269 , HOH A:473BINDING SITE FOR RESIDUE PO4 A 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AJ3)

(-) 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 3AJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3AJ3)

(-) 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:273
 aligned with PDLA_RHILO | Q988B9 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:273
                                                                                                                                                                                                                                                                                                    268      
                                    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      |  -   
           PDLA_RHILO     2 SDTKVYLLDGGSLVLDGYHVFWNRGPGGEVRFPVYSILIEHAEGRFLIDTGYDYDHVMKVLPFEKPIQEKHQTIPGALGLLGLEPRDIDVVVNSHFHFDHCGGNKYFPHAKKICHRSEVPQACNPQPFEHLGYSDLSFSAEAAEARGATAQLLEGTTRANSTFEGIDGDVDLARGVKLISTPGHSIGHYSLLVEFPRRKPILFTIDAAYTQKSLETLCQAAFHIDPVAGVNSMRKVKKLAEDHGAELMYSHDMDNFKTYRTGTQFYG------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeehhhhh.......eeeeeeeeeeeee..eeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhh.eee....hhhhh.hhhhh...eeeee.hhhhhhhh.hhhhh........hhhhhhhhhhhhhh..........eeee...eeee..eeeee........eeeee.......eeeeehhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aj3 A   2 SDTKVYLLDGGSLVLDGYHVFWNRGPGGEVRFPVYSILIEHAEGRFLIDTGYDYDHVmKVLPFEKPIQEKHQTIPGALGLLGLEPRDIDVVVNSHFHFDHCGGNKYFPHAKKICHRSEVPQACNPQPFEHLGYSDLSFSAEAAEARGATAQLLEGTTRANSTFEGIDGDVDLARGVKLISTPGHSIGHYSLLVEFPRRKPILFTIDAAYTQKSLETLCQAAFHIDPVAGVNSmRKVKKLAEDHGAELmYSHDmDNFKTYRTGTQFYGHHHHHH 274
                                    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   
                                                                                    59-MSE                                                                                                                                                                        234-MSE        249-MSE|                    
                                                                                                                                                                                                                                                                                      254-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 3AJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AJ3)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDLA_RHILO | Q988B9)
molecular function
    GO:0047585    4-pyridoxolactonase activity    Catalysis of the reaction: 4-pyridoxolactone + H(2)O = 4-pyridoxate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0042820    vitamin B6 catabolic process    The chemical reactions and pathways resulting in the breakdown of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDLA_RHILO | Q988B9: 4kep 4keq

(-) Related Entries Specified in the PDB File

3aj0 SAME NATIVE PROTEIN