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(-) Description

Title :  PCE REDUCTIVE DEHALOGENASE FROM S. MULTIVORANS IN COMPLEX WITH 2,4,6-TRICHLOROPHENOL
 
Authors :  C. Kunze, M. Bommer, W. R. Hagen, M. Uksa, H. Dobbek, T. Schubert, G. Diek
Date :  02 Nov 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1BVQ2Ligand/IonNORPSEUDO-B12
2GOL2Ligand/IonGLYCEROL
3SF44Ligand/IonIRON/SULFUR CLUSTER
4T6C2Ligand/Ion2,4,6-TRICHLOROPHENOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:290 , ARG A:291 , MET A:292 , PHE A:328 , CYS A:329 , CYS A:332 , LYS A:333 , CYS A:335 , CYS A:390 , PRO A:391 , PHE A:392binding 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 , VAL A:385 , 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 , 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 , SF4 A:502 , T6C A:505 , HOH A:630 , HOH A:666 , HOH A:671 , HOH A:675binding site for residue BVQ A 503
04AC4SOFTWAREPHE A:110 , PHE A:111 , LEU A:113 , MET A:254 , HOH A:601 , HOH A:620 , HOH A:627 , HOH A:640 , HOH A:646binding site for residue GOL A 504
05AC5SOFTWAREPHE A:38 , TRP A:56 , TRP A:96 , TYR A:102 , THR A:242 , TYR A:246 , ARG A:305 , TRP A:376 , TYR A:382 , BVQ A:503binding site for residue T6C A 505
06AC6SOFTWARESER B:290 , ARG B:291 , MET B:292 , PHE B:328 , CYS B:329 , CYS B:332 , LYS B:333 , CYS B:335 , CYS B:390 , PRO B:391 , PHE B:392binding site for residue SF4 B 501
07AC7SOFTWARECYS 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
08AC8SOFTWARETYR B:31 , THR B:36 , ALA B:37 , PHE B:38 , TYR B:170 , 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 , T6C B:505 , HOH B:636 , HOH B:672binding site for residue BVQ B 503
09AC9SOFTWAREPHE A:111 , PHE B:110 , LEU B:113 , MET B:119 , HOH B:648 , HOH B:653 , HOH B:655binding site for residue GOL B 504
10AD1SOFTWAREPHE B:38 , TRP B:56 , TYR B:102 , THR B:242 , TYR B:246 , ASN B:272 , ARG B:305 , TRP B:376 , TYR B:382 , BVQ B:503 , HOH B:642binding site for residue T6C B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MA1)

(-) 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 5MA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MA1)

(-) Exons   (0, 0)

(no "Exon" information available for 5MA1)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh........eee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhhheeeeeeee.....ee....eeee....eeeeeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhh...ee.....ee.......eeeeeeee............hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhh...hhhhhhh.....hhhhhh...hhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ma1 A  14 FAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINTYGLDADHFRDTVSFRKDRVK 462
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393||     439       449       459   
                                                                                                                                                                                                                                                                                                                                                                                                                      394|                               
                                                                                                                                                                                                                                                                                                                                                                                                                       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........eee.....eeehhhhhhhhhhhhhhh.eee..ee..hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeee.hhhhh..eeee.....hhhhhhhh.eeeeeeee.....ee....eeee....eeeeeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhh...ee.....ee.......eeeeeeee............hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhh...hhhhhhh.....hhhhhhh..hhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ma1 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 5MA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MA1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5MA1)

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  Cis Peptide Bonds
    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 5m90 5m91 5m92 5ma0 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