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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 4-BROMOPHENOL
 
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 :  1.90
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
1BEN1Ligand/IonBENZAMIDINE
2BML4Ligand/Ion4-BROMOPHENOL
3BVQ2Ligand/IonNORPSEUDO-B12
4GOL8Ligand/IonGLYCEROL
5SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:291 , 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
03AC3SOFTWAREILE A:22 , TYR 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:601 , HOH A:688 , HOH A:694 , HOH A:735 , HOH A:782 , HOH A:799 , HOH A:868binding site for residue BVQ A 503
04AC4SOFTWARETHR A:39 , PHE A:44 , GLU A:189 , ILE A:399binding site for residue BEN A 504
05AC5SOFTWAREPHE A:38 , PHE A:44 , TRP A:56 , ASN A:101 , GLU A:189 , HOH A:658 , HOH A:767binding site for residue GOL A 505
06AC6SOFTWAREPHE A:110 , LEU A:113 , MET A:119 , MET A:254 , HOH A:662 , HOH A:714 , HOH A:726 , HOH A:749 , HOH A:806 , PHE B:111binding site for residue GOL A 506
07AC7SOFTWAREGLU A:330 , PRO A:348 , ARG A:349 , HOH A:609 , HOH A:736binding site for residue GOL A 507
08AC8SOFTWAREARG A:349 , HOH A:645 , HOH A:657 , HOH A:722 , GLU B:172 , GLU B:191 , HOH B:680binding site for residue GOL A 508
09AC9SOFTWAREASP A:322 , HOH A:702 , HOH A:762 , HOH A:898 , PHE B:45binding site for residue GOL A 509
10AD1SOFTWAREARG A:354 , ASP A:368 , LYS A:371 , GLU B:378binding site for residue GOL A 510
11AD2SOFTWAREPHE A:111 , HOH A:620 , HOH A:628 , HOH A:689 , HOH A:894 , PHE B:110 , LEU B:113 , MET B:119 , HOH B:628binding site for residue GOL A 511
12AD3SOFTWAREPHE A:38 , TRP A:56 , TRP A:96 , TYR A:102 , TYR A:246 , ARG A:305 , TRP A:376 , TYR A:382 , HOH A:601binding site for residue BML A 512
13AD4SOFTWARELEU A:124 , LEU B:186 , HIS B:187binding site for residue BML A 513
14AD5SOFTWAREARG 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
15AD6SOFTWARECYS 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
16AD7SOFTWARETYR 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:601 , HOH B:610 , HOH B:623 , HOH B:661 , HOH B:704 , HOH B:746 , HOH B:805binding site for residue BVQ B 503
17AD8SOFTWAREPHE B:38 , THR B:39 , ASN B:101 , GLU B:189 , HOH B:634 , HOH B:643binding site for residue GOL B 504
18AD9SOFTWAREPHE B:38 , TRP B:56 , TRP B:96 , TYR B:102 , TYR B:246 , ASN B:272 , ARG B:305 , TRP B:376 , TYR B:382 , HOH B:601binding site for residue BML B 505
19AE1SOFTWARELEU A:186 , HIS A:187 , LEU B:124 , HOH B:895 , HOH B:904binding site for residue BML B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M8U)

(-) 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 5M8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M8U)

(-) Exons   (0, 0)

(no "Exon" information available for 5M8U)

(-) 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:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhh................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
                 5m8u A   1 AKEKNAAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNIWIHDGVEWLIDNTRFLNITEVWDGKINTYGLDADHFRDTVSFRKDRVK 462
                            ||      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       321       331       341       351       361       371       381       391       401       411 ||    438       448       458    
                            ||                                                                                                                                                                                                                                                                                                                                                                                                                       413|                               
                            1|                                                                                                                                                                                                                                                                                                                                                                                                                        431                               
                             3                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.................hhhhh........eee.....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
                 5m8u B   8 AEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINTYGLDADHFRDTVSFRKDRV 461
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      |433       443       453        
                                                                                                                                                                                                                                                                                                                                                                                                                            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 5M8U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M8U)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M8U)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        O68252_SULMU | O68252: 5m2g 5m8w 5ma2

(-) Related Entries Specified in the PDB File

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