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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 4-IODOPHENOL
 
Authors :  C. Kunze, M. Bommer, W. R. Hagen, M. Uksa, H. Dobbek, T. Schubert, G. Diek
Date :  03 Nov 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
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  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2BVQ2Ligand/IonNORPSEUDO-B12
3GOL6Ligand/IonGLYCEROL
4IOD2Ligand/IonIODIDE ION
5IOL8Ligand/Ion4-IODOPHENOL
6SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET 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: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:602 , HOH A:625 , HOH A:721 , HOH A:734 , HOH A:767 , HOH A:843binding 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 , ASN A:101 , GLU A:189 , HOH A:606 , HOH A:670binding site for residue GOL A 505
06AC6SOFTWAREPHE A:110 , LEU A:113 , MET A:119 , HOH A:631 , HOH A:643 , HOH A:780 , PHE B:111binding site for residue GOL A 506
07AC7SOFTWAREARG A:349 , PHE A:351 , HOH A:601 , HOH A:605 , GLU B:172binding site for residue GOL A 508
08AC8SOFTWAREPHE 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:602binding site for residue IOL A 509
09AC9SOFTWAREILE A:399 , HOH A:862binding site for residue IOL A 510
10AD1SOFTWARELEU A:58 , LEU A:186 , HIS A:187 , LEU B:124binding site for residue IOL A 511
11AD2SOFTWAREALA A:60 , LYS A:64 , GLY A:381 , TYR A:382binding site for residue IOD A 512
12AD3SOFTWAREARG 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
13AD4SOFTWARECYS 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
14AD5SOFTWARETYR 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:617 , HOH B:624 , HOH B:661 , HOH B:703 , HOH B:784 , HOH B:822binding site for residue BVQ B 503
15AD6SOFTWARETRP B:56 , PHE B:57 , LEU B:186 , GLU B:189 , HOH B:607 , HOH B:621binding site for residue GOL B 504
16AD7SOFTWAREPHE A:111 , PHE B:110 , LEU B:113 , MET B:119 , HOH B:610 , HOH B:629 , HOH B:733binding site for residue GOL B 505
17AD8SOFTWAREASP A:322 , PHE B:45 , HOH B:602binding site for residue IOL B 507
18AD9SOFTWARELEU A:124 , LEU B:186 , HIS B:187binding site for residue IOL B 508
19AE1SOFTWAREPHE B:38 , TRP B:56 , TYR B:102 , TYR B:246 , ARG B:305 , TRP B:376 , TYR B:382binding site for residue IOL B 509
20AE2SOFTWAREALA B:60 , LYS B:64 , TYR B:382binding site for residue IOD B 511
21AE3SOFTWAREPHE A:110 , LEU A:113 , MET A:119 , ASP A:322 , GLU A:327 , GLU A:330 , PRO A:348 , ARG A:349 , HOH A:631 , HOH A:643 , HOH A:679 , HOH A:780 , PRO B:41 , PHE B:45 , PHE B:111 , HOH B:602binding site for residues GOL A 507 and IOL B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MA2)

(-) 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 5MA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MA2)

(-) Exons   (0, 0)

(no "Exon" information available for 5MA2)

(-) 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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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
                 5ma2 A   1 AEKEKNAAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNIWIHDGVEWLIDNTRFLNITEVWDGKINTYGLDADHFRDTVSFRKDRVK 462
                                    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       320       330       340       350       360       370       380       390       400       410  ||   437       447       457     
                                                                                                                                                                                                                                                                                                                                                                                                                                                      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 .hhhhhh.................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
                 5ma2 B   8 AEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNITEVWDGKINTYGLDADHFRDTVSFRKDRV 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       432       442       452         
                                                                                                                                                                                                                                                                                                                                                                                                                             395|                              
                                                                                                                                                                                                                                                                                                                                                                                                                              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 5MA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MA2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5MA2)

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 Related Entries

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

UniProtKB/Swiss-Prot
        O68252_SULMU | O68252: 5m2g 5m8u 5m8w

(-) Related Entries Specified in the PDB File

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