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(-) Description

Title :  CRYSTAL STRUCTURE OF GKAP MUTANT G209D/R230H FROM GEOBACILLUS KAUSTOPHILUS HTA426
 
Authors :  J. An, Z. Zhang, Y. Zhang, Y. Feng, G. Wu
Date :  01 Sep 11  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphotriesterase, Lactonase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. An, Z. Zhang, Y. Zhang, Y. Feng, G. Wu
Engineering A Thermostable Lactonase For Enhanced Phosphotriesterase Activity Against Organophosphate Pesticides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A, B
    EC Number: 3.5.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GK1506
    Mutation: YES
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:23 , HIS A:25 , KCX A:145 , ASP A:266 , CO A:328 , HOH A:329BINDING SITE FOR RESIDUE CO A 327
2AC2SOFTWAREHIS B:23 , HIS B:25 , KCX B:145 , ASP B:266 , CO B:328 , HOH B:330BINDING SITE FOR RESIDUE CO B 327
3AC3SOFTWARETYR A:99 , KCX A:145 , HIS A:178 , HIS A:206 , CO A:327 , HOH A:329 , HOH A:332BINDING SITE FOR RESIDUE CO A 328
4AC4SOFTWARETYR B:99 , KCX B:145 , HIS B:178 , HIS B:206 , CO B:327 , HOH B:330 , HOH B:331BINDING SITE FOR RESIDUE CO B 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:236 -Val A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TNB)

(-) 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:324
 aligned with Q5KZU5_GEOKA | Q5KZU5 from UniProtKB/TrEMBL  Length:326

    Alignment length:324
                                    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       282       292       302       312       322    
         Q5KZU5_GEOKA     3 EMVETVCGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDESLRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIKLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
               SCOP domains d3tnba_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee.hhh..ee...eeee...hhhhhh.....hhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhh.eeeeee...hhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhh..........eeeee......hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee............hhhhhhhhhhhhhhh.hhh.eee....eeee.......hhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tnb A   3 EMVETVCGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDESLRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIkLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCDNTDPDYHRKTLAYGVYIAFDHFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
                                    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       282       292       302       312       322    
                                                                                                                                                                        145-KCX                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q5KZU5_GEOKA | Q5KZU5 from UniProtKB/TrEMBL  Length:326

    Alignment length:324
                                    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       282       292       302       312       322    
         Q5KZU5_GEOKA     3 EMVETVCGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDESLRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIKLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
               SCOP domains d3tnbb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee.hhh..ee...eeee...hhhhhh.....hhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhh.eeeeee...hhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhh..........eeeee......hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee............hhhhhhhhhhhhhhh.hhh.eee....eeee.......hhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tnb B   3 EMVETVCGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDESLRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIkLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCDNTDPDYHRKTLAYGVYIAFDHFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
                                    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       282       292       302       312       322    
                                                                                                                                                                        145-KCX
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5KZU5_GEOKA | Q5KZU5)
molecular function
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.

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    Met A:236 - Val A:237   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q5KZU5_GEOKA | Q5KZU5: 3ojg 3orw 3tn3 3tn4 3tn5 3tn6 4h9t 4h9u 4h9v 4h9x 4h9y 4h9z 4ha0 4wvx 5ch9

(-) Related Entries Specified in the PDB File

3tn3 3tn4 3tn5 3tn6