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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MERCURY-BOUND FORM OF MERB MUTANT C160S, 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 :  29 Oct 08  (Deposition) - 11 Nov 08  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Merb, Organomercurial Lyase, Alkylmercury Lyase, Mercury Resistance, 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
    Mutation: YES
    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  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:96 , ASP A:99 , CYS A:159 , HOH A:252BINDING SITE FOR RESIDUE HG A 221
2AC2SOFTWARECYS B:96 , ASP B:99 , PHE B:158 , CYS B:159 , HOH B:358BINDING SITE FOR RESIDUE HG B 221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F2H)

(-) 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 3F2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F2H)

(-) Exons   (0, 0)

(no "Exon" information available for 3F2H)

(-) 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:204
 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 d3f2ha1 A:1-80    Alkylmercury lyase MerB                                       d3f2ha2  A:81-208 Alkylmercury lyase MerB                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh---hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhh....ee.....eee..ee.....eeee.-..eeee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee.......hhhhhhhhhh.ee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f2h A   1 MKLAPYILELLTSVN---GTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEI-DRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCSHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMS 208
                                    10    |   20        30        40        50        60        70        80      | 90       100       110       120       130       140       150       160       170       180       190       200        
                                         15  19                                                                  87 |                                                                                                                       
                                                                                                                   89                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:202
 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 d3f2hb1 B:1-80     Alkylmercury lyase MerB                                      d3f2hb2   B:81-208 Alkylmercury lyase MerB                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.----hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh...ee.....eee..ee.....eeee.--..eee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee.......hhhhhhhhhh.ee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f2h B   1 MKLAPYILELLTSVN----TADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEI--RRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCSHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMS 208
                                    10    |   20        30        40        50        60        70        80      | 90       100       110       120       130       140       150       160       170       180       190       200        
                                         15   20                                                                 87 90
   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 3F2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F2H)

(-) 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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  3f2h
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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 3f0p 3f2f 3f2g 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 CRYSTAL STRUCTURE OF THE FREE FORM OF THE WILD TYPE PROTEIN
3f0p CRYSTAL STRUCTURE OF THE MERCURY-BOUND FORM OF THE WILD TYPE PROTEIN
3f2f
3f2g