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(-) Description

Title :  CRYSTAL STRUCTURE OF VMOLAC BOUND TO 3-OXO-C10 AHL
 
Authors :  J. Hiblot, J. Bzdrenga, C. Champion, G. Gotthard, D. Gonzalez, E. Chabr M. Elias
Date :  20 Sep 14  (Deposition) - 25 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lactonase, Quorum Sensing, Aryldialkylphosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hiblot, J. Bzdrenga, C. Champion, E. Chabriere, M. Elias
Crystal Structure Of Vmolac, A Tentative Quorum Quenching Lactonase From The Extremophilic Crenarchaeon Vulcanisaeta Moutnovskia.
Sci Rep V. 5 8372 2015
PubMed-ID: 25670483  |  Reference-DOI: 10.1038/SREP08372

(-) Compounds

Molecule 1 - PARATHION HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VMUT_2255
    Organism Scientific: VULCANISAETA MOUTNOVSKIA
    Organism Taxid: 985053
    Strain: 768-28

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric/Biological Unit (5, 23)
No.NameCountTypeFull Name
13M52Ligand/Ion3-OXO-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]DECANAMIDE
2CO4Ligand/IonCOBALT (II) ION
3GOL13Ligand/IonGLYCEROL
4KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5SO42Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:23 , HIS A:25 , KCX A:138 , ASP A:257 , CO A:402 , 3M5 A:403 , HOH A:830BINDING SITE FOR RESIDUE CO A 401
02AC2SOFTWAREKCX A:138 , HIS A:171 , HIS A:200 , ARG A:224 , CO A:401 , 3M5 A:403 , HOH A:830BINDING SITE FOR RESIDUE CO A 402
03AC3SOFTWAREHIS A:25 , LEU A:28 , TYR A:98 , KCX A:138 , HIS A:171 , ARG A:224 , ASP A:257 , ILE A:262 , TRP A:264 , TRP A:277 , CO A:401 , CO A:402 , HOH A:830BINDING SITE FOR RESIDUE 3M5 A 403
04AC4SOFTWAREALA A:53 , TYR A:258 , THR A:278 , MET A:279 , HOH A:554BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARELEU A:146 , ARG A:155 , ASP A:181 , ARG A:184 , GLU A:188BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARETHR A:99 , TYR A:100 , TRP A:264 , HOH A:524 , HOH A:543 , HOH A:616 , PHE B:105BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWARELEU A:180 , ARG A:184 , LYS A:187 , GLU A:216 , HOH A:709 , HOH A:727BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWAREARG A:110 , HOH A:561 , HOH A:585 , HOH A:738 , HOH A:795 , PRO B:266 , GOL B:406BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREALA A:194 , GLY A:217 , PHE A:219 , ASP A:250 , GLN A:251 , ARG A:310 , HOH A:640BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWARELEU A:40 , TYR A:41 , ILE A:262 , ASP A:263 , TYR A:265 , PRO A:267 , SO4 A:412 , HOH A:695 , HOH A:698 , ARG B:110 , HOH B:598BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWAREARG A:34 , PRO A:38 , HOH A:570 , HOH A:685 , HOH A:789BINDING SITE FOR RESIDUE GOL A 411
12BC3SOFTWAREPRO A:267 , GLU A:268 , GOL A:410 , ARG B:110 , HOH B:598BINDING SITE FOR RESIDUE SO4 A 412
13BC4SOFTWAREHIS B:23 , HIS B:25 , KCX B:138 , ASP B:257 , CO B:402 , 3M5 B:403 , HOH B:829BINDING SITE FOR RESIDUE CO B 401
14BC5SOFTWAREKCX B:138 , HIS B:171 , HIS B:200 , ARG B:224 , CO B:401 , 3M5 B:403 , HOH B:829BINDING SITE FOR RESIDUE CO B 402
15BC6SOFTWAREHIS B:25 , LEU B:28 , TYR B:98 , KCX B:138 , HIS B:171 , ARG B:224 , TYR B:230 , ASP B:257 , ILE B:262 , TRP B:264 , TYR B:265 , VAL B:269 , THR B:273 , TRP B:277 , CO B:401 , CO B:402 , HOH B:829BINDING SITE FOR RESIDUE 3M5 B 403
16BC7SOFTWAREGLY B:217 , ALA B:218 , PHE B:219 , ASP B:250 , ARG B:310 , HOH B:708 , HOH B:712 , HOH B:795BINDING SITE FOR RESIDUE GOL B 404
17BC8SOFTWAREALA B:53 , THR B:278 , MET B:279 , HOH B:560 , HOH B:631BINDING SITE FOR RESIDUE GOL B 405
18BC9SOFTWAREARG A:110 , GOL A:408 , HOH A:561 , LEU B:40 , TYR B:41 , THR B:261 , ILE B:262 , ASP B:263 , TYR B:265 , PRO B:267 , HOH B:556 , HOH B:630BINDING SITE FOR RESIDUE GOL B 406
19CC1SOFTWAREARG B:49 , TYR B:258 , CYS B:259 , PRO B:260 , PRO B:267 , HOH B:625 , HOH B:630 , HOH B:709 , HOH B:760BINDING SITE FOR RESIDUE GOL B 407
20CC2SOFTWAREASP B:250 , ARG B:302 , HOH B:576BINDING SITE FOR RESIDUE GOL B 408
21CC3SOFTWAREVAL B:174 , THR B:204 , ASP B:206 , PHE B:209BINDING SITE FOR RESIDUE SO4 B 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RDY)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eehhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhh.eee..ee.......hhhhhhhhhhhhhhhhhhhhhh...........eeee......hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.hhh.eee...........hhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdy A   2 VRISIAGGNEIDPGSMGLTLFHEHLRLITEVVRWNWPHLYNEDEELKRAIDAVNAAKKYGVKTIIDLTVAGIGCDVRFNEKVAKATGVNIIMGTGFYTYTEIPFYFKNRGIDSLVDAFVHDITIGIQGTNTRAAFVkAVIDSSGLTKDVEMAIRAAAKAHIKTDVPIITHSFVGNKSSLDLIRIFKEEGVDLARTVIGHVGDTDDISFIEQILREGAFIGLDRFGLDIYLPLDKRVKTAIELIKRGWIDQLLLSHDYCPTIDWYPPEVVRSTVPDWTMTLIFEKVIPRMRSEGITEEQINRVLIDNPRRLFTG 314
                                    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       281       291       301       311   
                                                                                                                                                                  138-KCX                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eehhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhh.eee..ee.......hhhhhh.hhhhhhhhhhhhhhh...........eeee......hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.hhh.eee...........hhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdy B   1 MVRISIAGGNEIDPGSMGLTLFHEHLRLITEVVRWNWPHLYNEDEELKRAIDAVNAAKKYGVKTIIDLTVAGIGCDVRFNEKVAKATGVNIIMGTGFYTYTEIPFYFKNRGIDSLVDAFVHDITIGIQGTNTRAAFVkAVIDSSGLTKDVEMAIRAAAKAHIKTDVPIITHSFVGNKSSLDLIRIFKEEGVDLARTVIGHVGDTDDISFIEQILREGAFIGLDRFGLDIYLPLDKRVKTAIELIKRGWIDQLLLSHDYCPTIDWYPPEVVRSTVPDWTMTLIFEKVIPRMRSEGITEEQINRVLIDNPRRLFTG 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
                                                                                                                                                                   138-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  (0, 0)

(no "SCOP Domain" information available for 4RDY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        F0QXN6_VULM7 | F0QXN6: 4rdz 4re0

(-) Related Entries Specified in the PDB File

4rdz CRYSTAL STRUCTURE OF VMOLAC IN P64 SPACE GROUP
4re0 CRYSTAL STRUCTURE OF VMOLAC IN P622 SPACE GROUP