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(-) Description

Title :  CRYSTAL STRUCTURE OF ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE MUTANT Y212F
 
Authors :  C. M. Daczkowski, S. D. Pegan, S. P. Harvey
Date :  19 May 15  (Deposition) - 14 Oct 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Opaa Organophosphate Prolidase Anhydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Daczkowski, S. D. Pegan, S. P. Harvey
Engineering The Organophosphorus Acid Anhydrolase Enzyme Fo Increased Catalytic Efficiency And Broadened Stereospecificity On Russian Vx.
Biochemistry V. 54 6423 2015
PubMed-ID: 26418828  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00624

(-) Compounds

Molecule 1 - OPAA ORGANOPHOSPHATE PROLIDASE ANHYDROLASE
    Chains: A, B
    EC Number: 3.4.13.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSE420
    Expression System Taxid: 562
    Gene: PEPQ, OPAA
    Mutation: YES
    Organism Scientific: ALTEROMONAS SP.
    Organism Taxid: 232
    Synonym: X-PRO DIPEPTIDASE,DFPASE,IMIDODIPEPTIDASE,ORGANOPHOSPHORUS ACID ANHYDROLASE 2,OPAA-2,PARAOXON HYDROLASE,PHOSPHOTRIESTERASE, PROLINE DIPEPTIDASE,PROLIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1BA3Ligand/IonBARIUM ION
2GOL1Ligand/IonGLYCEROL
3M442Ligand/IonN,N'-BIS(1-METHYLETHYL)PHOSPHORODIAMIDIC ACID
4MN7Ligand/IonMANGANESE (II) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:255 , HIS A:336 , GLU A:381 , GLU A:420 , MN A:502 , M44 A:508binding site for residue MN A 501
02AC2SOFTWAREASP A:244 , ASP A:255 , THR A:257 , GLU A:420 , MN A:501 , M44 A:508binding site for residue MN A 502
03AC3SOFTWAREHOH A:781binding site for residue BA A 503
04AC4SOFTWARELEU A:28 , HOH A:620 , HOH A:624binding site for residue MN A 504
05AC5SOFTWAREASP A:29 , HOH A:620 , HOH A:697binding site for residue MN A 505
06AC6SOFTWAREASP A:309binding site for residue BA A 506
07AC7SOFTWAREGLU A:134 , HOH A:729binding site for residue BA A 507
08AC8SOFTWAREPHE A:212 , ILE A:215 , LEU A:225 , ASP A:244 , ASP A:255 , HIS A:332 , HIS A:336 , HIS A:343 , GLU A:381 , GLU A:420 , MN A:501 , MN A:502binding site for residue M44 A 508
09AC9SOFTWAREASP B:244 , ASP B:255 , THR B:257 , GLU B:420 , MN B:502 , M44 B:504binding site for residue MN B 501
10AD1SOFTWAREASP B:255 , HIS B:336 , GLU B:381 , GLU B:420 , MN B:501 , M44 B:504binding site for residue MN B 502
11AD2SOFTWAREGLU B:10 , HOH B:646binding site for residue MN B 503
12AD3SOFTWAREPHE B:212 , ASP B:244 , ASP B:255 , HIS B:332 , HIS B:336 , HIS B:343 , GLU B:381 , GLU B:420 , MN B:501 , MN B:502binding site for residue M44 B 504
13AD4SOFTWAREGLU B:24 , ASN B:27 , HOH B:698binding site for residue GOL B 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZWP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZWP)

(-) 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:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh...eeeee..................hhhhhh..........eeee......eeeee.......hhhhhhheeeee.hhhhhhhh...hhh.eeee..hhhhhhhhh..ee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhh....eeee.hhhhh...............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhh.....eee..............................eeee..eee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..eeeee....eeehhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zwp A   3 KLAVLYAEHIATLQKRTREIIERENLDGVVFHSGQAKRQFLDDMYYPFKVNPQFKAWLPVIDNPHCWIVANGTDKPKLIFYRPVDFWNEYWADYFDIELLVKPDQVEKLLPYDKARFAYIGEYLEVAQALGFELMNPEPVMNFYHYHRAYKTQYELACMREANKIAVQGHKAARDAFFQGKSEFEIQQAYLLATQHSENDTPFGNIVALNENCAILHYTHFDRVAPATHRSFLIDAGANFNGYAADITRTYDFTGEGEFAELVATMKQHQIALCNQLAPGKLYGELHLDCHQRVAQTLSDFNIVNLSADEIVAKGITSTFFPHGLGHHIGLQVHDVGGFMADEQGAFLRCTRKIEANQVFTIEPGLYFIDSLLGDLAATDNNQHINWDKVAELKPFGGIRIEDNIIVHEDSLENMTRELELD 440
                                    12        22        32        42        52        62        72        82      ||99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349     ||368       378       388       398       408       418       428       438  
                                                                                                                 89|                                                                                                                                                                                                                                                               355|                                                                           
                                                                                                                  97                                                                                                                                                                                                                                                                365                                                                           


Chain B from PDB  Type:PROTEIN  Length:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...eeeee..................hhhhhh..........eeee......eeeee...........hhhhheeeee.hhhhh..........eeee..hhhhhhhh...ee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhh....eeee.hhhhh...............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh........................................eeee..eee.hhhhhhhhh...hhhhhhhhhhhhhh...eee..eeeee....eeehhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zwp B   2 NKLAVLYAEHIATLQKRTREIIERENLDGVVFHSGQAKRQFLDDMYYPFKVNPQFKAWLPVIDNPHCWIVANGTDKPKLIFYRPVDFWHPNEYWADYFDIELLVKPDQVEKLLPYDKARFAYIGEYLEVAQALGFELMNPEPVMNFYHYHRAYKTQYELACMREANKIAVQGHKAARDAFFQGKSEFEIQQAYLLATQHSENDTPFGNIVALNENCAILHYTHFDRVAPATHRSFLIDAGANFNGYAADITRTYDFTGEGEFAELVATMKQHQIALCNQLAPGKLYGELHLDCHQRVAQTLSDFNIVNLSADEIVAKGITSTFFPHGLGHHIGLQVHDVGGFMADEQGAHQEPPRCTRKIEANQVFTIEPGLYFIDSLLGDLAATDNNQHINWDKVAELKPFGGIRIEDNIIVHEDSLENMTRELELD 440
                                    11        21        31        41        51        61        71        81        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   ||  372       382       392       402       412       422       432        
                                                                                                                   90|                                                                                                                                                                                                                                                                     360|                                                                         
                                                                                                                    96                                                                                                                                                                                                                                                                      367
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
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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 4ZWP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  PEPQ_ALTSX | Q44238
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  3.4.13.9
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 Related Entries

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

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        PEPQ_ALTSX | Q44238: 3l24 3l7g 4zwo 4zwu

(-) Related Entries Specified in the PDB File

4zwp 4zwu