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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHOTRIESTERASE OPHC2 FROM PSEUDOMONAS PSEUDOALCALIGENES
 
Authors :  G. Gotthard, J. Hiblot, E. Chabriere, M. Elias
Date :  25 Jun 13  (Deposition) - 13 Nov 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Alpha Beta/Beta Alpha Sandwich, Metallo-Hydrolase, Phosphotriesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Gotthard, J. Hiblot, D. Gonzalez, M. Elias, E. Chabriere
Structural And Enzymatic Characterization Of The Phosphotriesterase Ophc2 From Pseudomonas Pseudoalcaligenes
Plos One V. 8 77995 2013
PubMed-ID: 24223749  |  Reference-DOI: 10.1371/JOURNAL.PONE.0077995
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORGANOPHOSPHORUS HYDROLASE
    Chains: A, B, C, D, E
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22-B(+)
    Expression System Strain: BL21(DE3)-PGRO7/GROEL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OPHC2
    Organism Scientific: PSEUDOMONAS PSEUDOALCALIGENES
    Organism Taxid: 330

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): A    
Biological Unit 2 (1x):  BC  
Biological Unit 3 (1x):    DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric Unit (4, 23)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL8Ligand/IonGLYCEROL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4ZN10Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL4Ligand/IonGLYCEROL
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
3PGE-1Ligand/IonTRIETHYLENE GLYCOL
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PGE-1Ligand/IonTRIETHYLENE GLYCOL
4ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:116 , VAL A:118 , GLN A:119 , GLY A:147 , VAL A:149 , ASN A:150 , ALA A:156 , HOH A:515 , HOH A:521 , HOH A:553 , HOH A:565BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREPHE A:111 , PHE B:111 , GOL B:401BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREALA A:222 , PRO A:224 , PRO A:228 , GLY A:229 , HIS A:230 , THR A:231 , HOH A:723BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREHIS A:141 , PHE A:265 , VAL A:267 , ASP B:56 , PHE B:111 , THR B:114 , ASP C:323 , HOH C:594BINDING SITE FOR RESIDUE PGE A 404
05AC5SOFTWAREHIS A:139 , HIS A:141 , HIS A:226 , ASP A:247 , ZN A:406 , HOH A:700 , HOH A:825BINDING SITE FOR RESIDUE ZN A 405
06AC6SOFTWAREASP A:143 , HIS A:144 , ASP A:247 , HIS A:294 , ZN A:405 , HOH A:700BINDING SITE FOR RESIDUE ZN A 406
07AC7SOFTWAREPHE A:111 , HIS B:141 , PHE B:265BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREPHE A:111 , GOL A:402 , PHE B:111 , ASP B:143 , PHE B:265 , HOH B:663BINDING SITE FOR RESIDUE GOL B 401
09AC9SOFTWAREGLN B:109 , VAL B:149 , ASN B:150 , ALA B:151 , GLY B:153 , HOH B:603BINDING SITE FOR RESIDUE GOL B 402
10BC1SOFTWAREGLY B:116 , VAL B:118 , GLN B:119 , GLY B:147 , VAL B:149 , ASN B:150 , ALA B:156 , HOH B:514 , HOH B:530 , HOH B:541BINDING SITE FOR RESIDUE GOL B 403
11BC2SOFTWAREPRO B:296 , PRO B:298 , GLY B:299 , LEU B:300 , TRP B:312 , PRO B:314 , HOH B:531 , HOH B:558BINDING SITE FOR RESIDUE EDO B 404
12BC3SOFTWAREASP B:143 , HIS B:144 , ASP B:247 , HIS B:294 , ZN B:406 , HOH B:600BINDING SITE FOR RESIDUE ZN B 405
13BC4SOFTWAREHIS B:139 , HIS B:141 , HIS B:226 , ASP B:247 , ZN B:405 , HOH B:600 , HOH B:663BINDING SITE FOR RESIDUE ZN B 406
14BC5SOFTWAREGLY C:116 , GLN C:119 , GLY C:147 , VAL C:149 , ASN C:150 , ALA C:156 , HOH C:522 , HOH C:529 , HOH C:563BINDING SITE FOR RESIDUE GOL C 401
15BC6SOFTWARELEU C:140 , HOH C:553 , VAL D:149 , ALA D:151BINDING SITE FOR RESIDUE GOL C 402
16BC7SOFTWAREARG C:76 , ALA C:311 , TRP C:312BINDING SITE FOR RESIDUE EDO C 403
17BC8SOFTWAREHIS C:139 , HIS C:141 , HIS C:226 , ASP C:247 , ZN C:405 , HOH C:635BINDING SITE FOR RESIDUE ZN C 404
18BC9SOFTWAREASP C:143 , HIS C:144 , ASP C:247 , HIS C:294 , ZN C:404 , HOH C:635BINDING SITE FOR RESIDUE ZN C 405
19CC1SOFTWARETHR D:105 , GLY D:116 , VAL D:118 , GLN D:119 , GLY D:147 , VAL D:149 , ASN D:150 , ALA D:156 , HOH D:504 , HOH D:514BINDING SITE FOR RESIDUE GOL D 401
20CC2SOFTWAREHIS D:139 , HIS D:141 , HIS D:226 , ASP D:247 , ZN D:403 , HOH D:541BINDING SITE FOR RESIDUE ZN D 402
21CC3SOFTWAREASP D:143 , HIS D:144 , ASP D:247 , HIS D:294 , ZN D:402 , HOH D:541BINDING SITE FOR RESIDUE ZN D 403
22CC4SOFTWAREHIS E:139 , HIS E:141 , HIS E:226 , ASP E:247 , ZN E:402 , HOH E:504BINDING SITE FOR RESIDUE ZN E 401
23CC5SOFTWAREASP E:143 , HIS E:144 , ASP E:247 , HIS E:294 , ZN E:401 , HOH E:510BINDING SITE FOR RESIDUE ZN E 402

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:110 -A:146
2B:110 -B:146
3C:110 -C:146
4D:110 -D:146
5E:110 -E:146

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe A:297 -Pro A:298
2Phe B:297 -Pro B:298
3Phe C:297 -Pro C:298
4Phe D:297 -Pro D:298
5Phe E:297 -Pro E:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LE6)

(-) Exons   (0, 0)

(no "Exon" information available for 4LE6)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4le6a_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee..eeeeeeeeeeeeehhh.ee..hhhhhhhhhhhh.......eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhhhhh...........eee...........eeeee........eeeeeee..eeeeeee....hhhhhh.....ee....hhhhhhhhhhhhhhhhhhhh.eeee.......eeeeee....eeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le6 A  25 AAPAQQKTQVPGYYRMALGDFEVTALYDGYVDLPASLLKGIDDKDLQSLLARMFVASEKGVQTAVNAYLINTGDNLVLIDTGAAQCFGPTLGVVQTNLKASGYQPEQVDTVLLTHLHPDHACGLVNADGSPAYPNATVEVPQAEGELLPGVSLVASPGHTPGHTSYLFKSGGQSLLVWGDILLNHAVQFAKPEVVFEFDVDSDQARQSRQRILAEAATDKLWVAGAHLPFPGLGHVRKEAQGYAWVPVEFSPIRSDR 324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164  ||   217       227       237       247       257       267       277       287       297       307       317       
                                                                                                                                                                        167|                                                                                                                 
                                                                                                                                                                         211                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4le6b_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee..eeeeeeeeeeeeehhh.ee..hhhhhhhhhhhh.......eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhhhhh...........eee.........eeeee........eeeeeee..eeeeeee....hhhhhh.....ee....hhhhhhhhhhhhhhhhhhhh.eeee.......eeeeee....eeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le6 B  25 AAPAQQKTQVPGYYRMALGDFEVTALYDGYVDLPASLLKGIDDKDLQSLLARMFVASEKGVQTAVNAYLINTGDNLVLIDTGAAQCFGPTLGVVQTNLKASGYQPEQVDTVLLTHLHPDHACGLVNADGSPAYPNATVEVPQAELLPGVSLVASPGHTPGHTSYLFKSGGQSLLVWGDILLNHAVQFAKPEVVFEFDVDSDQARQSRQRILAEAATDKLWVAGAHLPFPGLGHVRKEAQGYAWVPVEFSPIRSDR 324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164  ||   219       229       239       249       259       269       279       289       299       309       319     
                                                                                                                                                                        167|                                                                                                               
                                                                                                                                                                         213                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains d4le6c_ C: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeeeeeeeeehhh.ee..hhhhhhhhhhhh.......eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhhhhh...........eee.........eeeee........eeeeeee..eeeeeee...............ee....hhhhhhhhhhhhhhhhhhhh.eeee.......eeeeee....eeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le6 C  26 APAQQKTQVPGYYRMALGDFEVTALYDGYVDLPASLLKGIDDKDLQSLLARMFVASEKGVQTAVNAYLINTGDNLVLIDTGAAQCFGPTLGVVQTNLKASGYQPEQVDTVLLTHLHPDHACGLVNADGSPAYPNATVEVPQAELLPGVSLVASPGHTPGHTSYLFKSGGQSLLVWGDILLNHAVQFAKPEVVFEFDVDSDQARQSRQRILAEAATDKLWVAGAHLPFPGLGHVRKEAQGYAWVPVEFSPIRSDR 324
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165 ||    220       230       240       250       260       270       280       290       300       310       320    
                                                                                                                                                                       167|                                                                                                               
                                                                                                                                                                        213                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4le6d_ D: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeeeeeeeeehhh.ee..hhhhhhhhhhh........eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhhhhh...........eee.......eeeee........eeeeeee..eeeeeee....hhhhhh.....ee....hhhhhhhhhhhhhhhhhhhh.eeee.......eeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le6 D  26 APAQQKTQVPGYYRMALGDFEVTALYDGYVDLPASLLKGIDDKDLQSLLARMFVASEKGVQTAVNAYLINTGDNLVLIDTGAAQCFGPTLGVVQTNLKASGYQPEQVDTVLLTHLHPDHACGLVNADGSPAYPNATVEVPQLLPGVSLVASPGHTPGHTSYLFKSGGQSLLVWGDILLNHAVQFAKPEVVFEFDVDSDQARQSRQRILAEAATDKLWVAGAHLPFPGLGHVRKEAQGYAWVPVEFSPIRSD 323
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165||     222       232       242       252       262       272       282       292       302       312       322 
                                                                                                                                                                      166|                                                                                                             
                                                                                                                                                                       214                                                                                                             


Chain E from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4le6e_ E: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eeeeeeeeeeee....ee.......hhhhhh........eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh........hhhhhhhhh......................eeee........eeeeeee..eeeee......hhhhhh.....ee......hhhhhhhhhhhhhhhhhh.eee........eeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le6 E  26 APAQQKTQVPGYYRMALGDFEVTALYDGYVDLPASLLKGIDDKDLQSLLARMFVASEKGVQTAVNAYLINTGDNLVLIDTGAAQCFGPTLGVVQTNLKASGYQPEQVDTVLLTHLHPDHACGLVNADGSPAYPNATVEVPQLLPGVSLVASPGHTPGHTSYLFKSGGQSLLVWGDILLNHAVQFAKPEVVFEFDVDSDQARQSRQRILAEAATDKLWVAGAHLPFPGLGHVRKEAQGYAWVPVEFSPIRSD 323
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165||     222       232       242       252       262       272       282       292       302       312       322 
                                                                                                                                                                      166|                                                                                                             
                                                                                                                                                                       214
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  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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LE6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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