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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 4-CHLOROPHENOL
 
Authors :  C. Kunze, M. Bommer, W. R. Hagen, M. Uksa, H. Dobbek, T. Schubert, G. Diek
Date :  30 Oct 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
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 CATALYTICALLY ACTIVE SUBUNIT
    Chains: A, B
    Organism Scientific: SULFUROSPIRILLUM MULTIVORANS
    Organism Taxid: 66821

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
14CH2Ligand/Ion4-CHLOROPHENOL
2BEN3Ligand/IonBENZAMIDINE
3BVQ2Ligand/IonNORPSEUDO-B12
4GOL8Ligand/IonGLYCEROL
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 , ILE A:344 , 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: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 , 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 , SF4 A:502 , HOH A:656 , HOH A:658 , HOH A:680 , HOH A:766binding site for residue BVQ A 503
04AC4SOFTWAREPHE A:110 , MET A:119 , HOH A:667 , HOH A:720 , HOH A:723 , HOH A:794 , PHE B:111binding site for residue GOL A 506
05AC5SOFTWAREARG A:349 , HOH A:727 , GLU B:172 , GLU B:191 , HOH B:714binding site for residue GOL A 508
06AC6SOFTWAREASP A:322 , HOH A:668binding site for residue GOL A 509
07AC7SOFTWAREARG A:354 , ASP A:368 , LYS A:371 , GLU B:378binding site for residue GOL A 510
08AC8SOFTWAREVAL A:34 , THR A:39 , GLU A:189 , HIS A:400 , BEN A:504binding site for residue BEN A 511
09AC9SOFTWAREPHE A:38 , TRP A:56 , TRP A:96 , TYR A:102 , TYR A:246 , ARG A:305 , TRP A:376 , TYR A:382binding site for residue 4CH A 512
10AD1SOFTWAREMET B:292 , PHE B:328 , CYS B:329 , CYS B:332 , LYS B:333 , CYS B:335 , CYS B:390binding 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 , VAL B:387 , SF4 B:502 , HOH B:614 , HOH B:620 , HOH B:634 , HOH B:693 , HOH B:715binding site for residue BVQ B 503
13AD4SOFTWAREPHE B:38 , TRP B:56 , LEU B:186 , GLU B:189 , HOH B:602 , HOH B:701binding site for residue GOL B 504
14AD5SOFTWAREPHE A:111 , PHE B:110 , LEU B:113 , MET B:119 , HOH B:608 , HOH B:613 , HOH B:616 , HOH B:686 , HOH B:723binding site for residue GOL B 505
15AD6SOFTWAREPHE B:38 , TRP B:56 , TRP B:96 , TYR B:102 , TYR B:246 , ARG B:305 , TRP B:376binding site for residue 4CH B 507
16AD7SOFTWAREPHE A:38 , THR A:39 , PHE A:44 , ASN A:101 , GLU A:189 , ASP A:408 , BEN A:511binding site for residues BEN A 504 and GOL A 505
17AD8SOFTWAREPHE A:110 , MET A:119 , GLU A:330 , PRO A:348 , ARG A:349 , HOH A:601 , HOH A:667 , HOH A:720 , HOH A:723 , HOH A:759 , HOH A:794 , PHE B:38 , THR B:39 , PRO B:41 , TRP B:56 , TRP B:96 , TYR B:102 , PHE B:111 , GLU B:189 , GLU B:191 , TYR B:246 , ARG B:305 , TRP B:376binding site for residues GOL A 507 and BEN B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M8W)

(-) 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 5M8W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M8W)

(-) Exons   (0, 0)

(no "Exon" information available for 5M8W)

(-) 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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               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.hhhhhhh..hhhhh...hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m8w A   3 KEKNAAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNIWIHDGVEWLIDNTRFLNITEVWDGKINTYGLDADHFRDTVSFRKDRVK 462
                                    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       332       342       352       362       372       382       392       402       412||     439       449       459   
                                                                                                                                                                                                                                                                                                                                                                                                                                                    413|                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                     431                               


Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.................hhhhh...hhhhheee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhh......................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhh.eeeeeeee.....ee....eeee....eeeeeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhh...ee.....ee.......eeeeeeee............hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhh..hhhhh...hhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m8w B   7 AAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINTYGLDADHFRDTVSFRKDRV 461
                                    16        26        36        46        56        66        76        86        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       366       376       386       432       442       452         
                                                                                                                                                                                                                                                                                                                                                                                                                             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 5M8W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M8W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M8W)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M8W)

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 Related Entries

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

UniProtKB/Swiss-Prot
        O68252_SULMU | O68252: 5m2g 5m8u 5ma2

(-) Related Entries Specified in the PDB File

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