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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MERCURY-BOUND FORM OF MERB, THE ORGANOMERCURIAL LYASE INVOLVED IN A BACTERIAL MERCURY RESISTANCE SYSTEM
 
Authors :  J. Lafrance-Vanasse, M. Lefebvre, P. Di Lello, J. Sygusch, J. G. Omichinski
Date :  25 Oct 08  (Deposition) - 11 Nov 08  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Merb, Organomercurial Lyase, Alkylmercury Lyase, Mercury Resistance, Phmba, Mercuric Resistance, Plasmid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lafrance-Vanasse, M. Lefebvre, P. Di Lello, J. Sygusch, J. G. Omichinski
Crystal Structures Of The Organomercurial Lyase Merb In Its Free And Mercury-Bound Forms: Insights Into The Mechanism Of Methylmercury Degradation
J. Biol. Chem. V. 284 938 2009
PubMed-ID: 19004822  |  Reference-DOI: 10.1074/JBC.M807143200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALKYLMERCURY LYASE
    Chains: A, B
    EC Number: 4.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MERB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ORGANOMERCURIAL LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BR1Ligand/IonBROMIDE ION
2HG2Ligand/IonMERCURY (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2HG-1Ligand/IonMERCURY (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2HG-1Ligand/IonMERCURY (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:96 , ASP A:99 , CYS A:159 , HOH A:214BINDING SITE FOR RESIDUE HG A 213
2AC2SOFTWAREPRO A:5BINDING SITE FOR RESIDUE BR B 213
3AC3SOFTWARECYS B:96 , ASP B:99 , CYS B:159 , HOH B:219BINDING SITE FOR RESIDUE HG B 214

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F0P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:137 -Pro A:138
2Glu B:137 -Pro B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F0P)

(-) Exons   (0, 0)

(no "Exon" information available for 3F0P)

(-) Sequences/Alignments

Asymmetric 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:208
 aligned with MERB_ECOLX | P77072 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           MERB_ECOLX     1 MKLAPYILELLTSVNRTNGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMS 208
               SCOP domains d3f0pa1 A:1-80 Alkylmercury lyase MerB                                          d3f0pa2 A:81-208 Alkylmercury lyase MerB                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh...ee.....eee..ee.....eeeee..eeeee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee.......hhhhhhhhhh.ee.hhhhhhhhhh........eeeehhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0p A   1 MKLAPYILELLTSVNRTNGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMS 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with MERB_ECOLX | P77072 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           MERB_ECOLX     1 MKLAPYILELLTSVNRTNGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLL 204
               SCOP domains d3f0pb1 B:1-      80 Alkylmercury lyase MerB                                    d3f0pb2 B:81-204 Alkylmercury lyase MerB                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh------hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh...ee.....eee..ee.....eeeee..eeeee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee...---.hhhhhhhhhh.ee.hhhhhhhhhh........eeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f0p B   1 MKLAPYILELLT------GTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLP---ADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLL 204
                                    10 |      20        30        40        50        60        70        80        90       100       110       120       130       140       | - |     160       170       180       190       200    
                                      12     19                                                                                                                              148 152
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F0P)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MERB_ECOLX | P77072)
molecular function
    GO:0018836    alkylmercury lyase activity    Catalysis of the reaction: R-Hg+ + H+ = R-H + Hg2+.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0046413    organomercury catabolic process    The chemical reactions and pathways resulting in the breakdown of organomercury compounds, any organic compound containing a mercury atom.
    GO:0046689    response to mercury ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.

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  3f0p
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  4.99.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        MERB_ECOLX | P77072: 1s6l 3f0o 3f2f 3f2g 3f2h 3fn8 5c0t 5c0u 5dsf 5u79 5u7a 5u7b 5u7c 5u82 5u83 5u88

(-) Related Entries Specified in the PDB File

1s6l NMR SOLUTION STRUCTURE OF THE SAME PROTEIN
3f0o