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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 3,4,5-TRIFLUOROPHENOL
 
Authors :  C. Kunze, M. Bommer, W. R. Hagen, M. Uksa, H. Dobbek, T. Schubert, G. Diek
Date :  31 Oct 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Organohalide Respiration Anaerobic Crystallisation Cobalamin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kunze, M. Bommer, W. R. Hagen, M. Uksa, H. Dobbek, T. Schubert, G. Diekert
Cobamide-Mediated Enzymatic Reductive Dehalogenation Via Long-Range Electron Transfer.
Nat Commun V. 8 15858 2017
PubMed-ID: 28671181  |  Reference-DOI: 10.1038/NCOMMS15858

(-) Compounds

Molecule 1 - TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA
    Chains: A, B
    Organism Scientific: SULFUROSPIRILLUM MULTIVORANS DSM 12446
    Organism Taxid: 1150621

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2BVQ2Ligand/IonNORPSEUDO-B12
3GOL5Ligand/IonGLYCEROL
4JIF3Ligand/Ion3,4,5-TRIS(FLUORANYL)PHENOL
5SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:291 , MET A:292 , CYS A:329 , CYS A:332 , LYS A:333 , CYS A:335 , CYS A:390binding site for residue SF4 A 501
02AC2SOFTWARECYS A:339 , PRO A:340 , SER A:341 , CYS A:372 , CYS A:383 , GLY A:384 , CYS A:386 , BVQ A:503binding site for residue SF4 A 502
03AC3SOFTWARETYR A:31 , THR A:36 , ALA A:37 , PHE A:38 , TYR A:170 , THR A:242 , TYR A:246 , MET A:249 , ASN A:272 , GLY A:275 , GLN A:276 , SER A:277 , VAL A:278 , ALA A:279 , ALA A:289 , MET A:292 , GLY A:293 , ALA A:294 , CYS A:295 , PRO A:302 , VAL A:304 , ARG A:305 , LEU A:306 , LYS A:308 , HIS A:357 , ASN A:358 , GLN A:359 , LYS A:362 , GLN A:364 , TYR A:369 , CYS A:372 , TRP A:376 , TYR A:382 , VAL A:387 , SF4 A:502 , HOH A:644 , HOH A:673 , HOH A:717 , HOH A:761 , HOH A:764 , HOH A:787 , HOH A:817binding site for residue BVQ A 503
04AC4SOFTWAREPHE A:38 , PHE A:44 , TRP A:56 , GLU A:189 , HOH A:775 , HOH A:878binding site for residue GOL A 504
05AC5SOFTWAREPHE A:110 , LEU A:113 , MET A:119 , MET A:254 , HOH A:709 , HOH A:711 , HOH A:719 , HOH A:721 , HOH A:747 , PHE B:111binding site for residue GOL A 505
06AC6SOFTWAREARG A:349 , HOH A:643 , HOH A:781 , HOH A:848 , GLU B:172 , GLU B:191binding site for residue GOL A 506
07AC7SOFTWAREASP A:322 , GLY A:324 , HOH A:701binding site for residue GOL A 507
08AC8SOFTWAREVAL A:34 , THR A:39 , PRO A:41 , GLU A:189binding site for residue BEN A 508
09AC9SOFTWAREPHE A:38 , TRP A:56 , TRP A:96 , TYR A:102 , THR A:242 , TYR A:246 , ASN A:272 , TRP A:376 , TYR A:382 , HOH A:731 , HOH A:817binding site for residue JIF A 509
10AD1SOFTWAREARG B:291 , MET B:292 , PHE B:328 , CYS B:329 , CYS B:332 , LYS B:333 , CYS B:335 , CYS B:390 , PHE B:392binding site for residue SF4 B 501
11AD2SOFTWARECYS B:339 , PRO B:340 , SER B:341 , CYS B:372 , CYS B:383 , GLY B:384 , CYS B:386 , BVQ B:503binding site for residue SF4 B 502
12AD3SOFTWARETYR B:31 , THR B:36 , ALA B:37 , PHE B:38 , TYR B:170 , THR B:242 , TYR B:246 , MET B:249 , ASN B:272 , GLY B:275 , GLN B:276 , SER B:277 , VAL B:278 , ALA B:289 , MET B:292 , GLY B:293 , ALA B:294 , CYS B:295 , PRO B:302 , VAL B:304 , ARG B:305 , LEU B:306 , LYS B:308 , HIS B:357 , ASN B:358 , GLN B:359 , LYS B:362 , GLN B:364 , TYR B:369 , CYS B:372 , TRP B:376 , TYR B:382 , SF4 B:502 , HOH B:644 , HOH B:650 , HOH B:671 , HOH B:694 , HOH B:717 , HOH B:751 , HOH B:828binding site for residue BVQ B 503
13AD4SOFTWAREPHE A:111 , PHE B:110 , LEU B:113 , MET B:119 , MET B:254 , HOH B:651 , HOH B:652 , HOH B:656 , HOH B:748 , HOH B:753binding site for residue GOL B 504
14AD5SOFTWAREASP A:322 , PHE B:44 , LEU B:186 , HIS B:187 , HOH B:603 , HOH B:604binding site for residue BEN B 505
15AD6SOFTWAREGLU A:327 , THR B:39 , PHE B:44 , PHE B:45 , GLU B:189 , JIF B:508 , HOH B:604binding site for residue BEN B 506
16AD7SOFTWAREPHE B:38 , TRP B:56 , TRP B:96 , TYR B:102 , TYR B:246 , ASN B:272 , TRP B:376 , TYR B:382 , HOH B:671 , HOH B:885binding site for residue JIF B 507
17AD8SOFTWAREVAL B:34 , THR B:39 , PRO B:41 , VAL B:174 , GLU B:189 , ILE B:190 , GLU B:191 , BEN B:506 , HOH B:857 , HOH B:872binding site for residue JIF B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M90)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:233 -Pro A:234
2Ala B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M90)

(-) Exons   (0, 0)

(no "Exon" information available for 5M90)

(-) 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:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.................hhhhh...hhhhheee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhh.eeeeeeee.....ee....eeee....eeeeeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhh...ee.....ee.......eeeeeeee............hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhh...hhhhhhhhhhh...eee....eee.hhhhh.hhhhhh...hhhhh...hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m90 A   5 KNAAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNIWIHDGVEWLIDNTRFLNITEVWDGKINTYGLDADHFRDTVSFRKDRVK 462
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       431       441       451       461 
                                                                                                                                                                                                                                                                                                                                                                                                                                                  413|                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                   431                               


Chain B from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhh...hhhhheee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhhheeeeeeee.....ee....eeee....eeeeeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhh...ee.....ee.......eeeeeeee............hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh...hhhhh...hhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m90 B  10 IRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINTYGLDADHFRDTVSFRKDRV 461
                                    19        29        39        49        59        69        79        89        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       359       369       379       389    || 435       445       455      
                                                                                                                                                                                                                                                                                                                                                                                                                          394|                              
                                                                                                                                                                                                                                                                                                                                                                                                                           431
   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 5M90)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M90)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M90)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M90)

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    Ala A:233 - Pro A:234   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        W6EQP0_SULMU | W6EQP0: 5m8x 5m8y 5m8z 5m91 5m92 5ma0 5ma1 5maa
UniProtKB/TrEMBL
        W6EQP0_SULMU | W6EQP0: 4uqu 4ur0 4ur1 4ur2 4ur3

(-) Related Entries Specified in the PDB File

5m2g 5M2G CONTAINS THE SAME PROTEIN COMPLEXED WITH 2,4,6-TRIBROMOPHENOL