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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 2,4-DIBROMOPHENOL
 
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 :  1.79
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  (6, 21)

Asymmetric/Biological Unit (6, 21)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2BR1Ligand/IonBROMIDE ION
3BVQ2Ligand/IonNORPSEUDO-B12
4GOL7Ligand/IonGLYCEROL
5SF44Ligand/IonIRON/SULFUR CLUSTER
6Y8I4Ligand/Ion2,4-BIS(BROMANYL)PHENOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:290 , ARG 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
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 , 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 , Y8I A:512 , HOH A:605 , HOH A:618 , HOH A:697 , HOH A:740 , HOH A:744 , HOH A:792binding site for residue BVQ A 503
04AC4SOFTWARETHR A:39 , PHE A:44 , GLU A:189 , ASP A:408 , GOL A:505 , BEN A:511binding site for residue BEN A 504
05AC5SOFTWARETHR A:39 , ASN A:101 , GLU A:189 , BEN A:504 , HOH A:839 , HOH A:853binding site for residue GOL A 505
06AC6SOFTWAREPHE A:110 , LEU A:113 , MET A:119 , MET A:254 , HOH A:632 , HOH A:643 , HOH A:725 , HOH A:752 , HOH A:775 , PHE B:111binding site for residue GOL A 506
07AC7SOFTWAREGLU A:330 , PRO A:348 , ARG A:349 , HOH A:635 , HOH A:669 , HOH A:745 , BEN B:505binding site for residue GOL A 507
08AC8SOFTWAREARG A:349 , THR A:350 , HOH A:721 , HOH A:784 , GLU B:172 , GLU B:191 , HOH B:622binding site for residue GOL A 508
09AC9SOFTWAREASP A:322 , HOH A:651 , PHE B:45binding site for residue GOL A 509
10AD1SOFTWAREPHE A:111 , HOH A:631 , HOH A:675 , HOH A:699 , PHE B:110 , LEU B:113 , MET B:119 , HOH B:654binding site for residue GOL A 510
11AD2SOFTWAREVAL A:34 , THR A:39 , GLU A:189 , BEN A:504binding site for residue BEN A 511
12AD3SOFTWAREPHE A:38 , TRP A:56 , TYR A:102 , THR A:242 , TYR A:246 , ASN A:272 , TRP A:376 , TYR A:382 , BVQ A:503 , HOH A:605binding site for residue Y8I A 512
13AD4SOFTWAREPHE A:57 , LEU A:186 , HIS A:187 , HOH A:1017 , LEU B:124binding site for residue Y8I A 513
14AD5SOFTWAREPHE A:44 , LEU A:186binding site for residue BR A 514
15AD6SOFTWAREARG B:291 , MET 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
16AD7SOFTWARECYS 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
17AD8SOFTWARETYR 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 , TYR B:382 , VAL B:387 , SF4 B:502 , Y8I B:506 , HOH B:604 , HOH B:605 , HOH B:650 , HOH B:660 , HOH B:671 , HOH B:689 , HOH B:744binding site for residue BVQ B 503
18AD9SOFTWAREPHE B:38 , ASN B:101 , LEU B:186 , GLU B:189 , HOH B:692binding site for residue GOL B 504
19AE1SOFTWAREGLU A:330 , GOL A:507 , VAL B:34 , THR B:39 , PRO B:41 , GLU B:189 , GLU B:191binding site for residue BEN B 505
20AE2SOFTWAREPHE B:38 , TRP B:56 , TYR B:102 , THR B:242 , TYR B:246 , ASN B:272 , TRP B:376 , TYR B:382 , BVQ B:503 , HOH B:604binding site for residue Y8I B 506
21AE3SOFTWARELEU A:124 , LEU B:186 , HIS B:187 , HOH B:641binding site for residue Y8I B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M92)

(-) 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 5M92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M92)

(-) Exons   (0, 0)

(no "Exon" information available for 5M92)

(-) 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 ...hhhhhhhhhh................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...eee....eee.hhhhh.hhhhhh...hhhhh...hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m92 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........eee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhh.eeeeeeee.....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
                 5m92 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)
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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  (0, 0)

(no "SCOP Domain" information available for 5M92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M92)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M92)

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  5m92
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  W6EQP0_SULMU | W6EQP0
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 Related Entries

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

UniProtKB/Swiss-Prot
        W6EQP0_SULMU | W6EQP0: 5m8x 5m8y 5m8z 5m90 5m91 5ma0 5ma1 5maa
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        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