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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LEAD-BOUND FORM OF MERB FORMED FROM DIETHYLLEAD.
 
Authors :  H. M. Wahba, M. Stevenson, A. Mansour, J. Sygusch, D. E. Wilcox, J. G. Omi
Date :  12 Dec 16  (Deposition) - 11 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacterial Proteins, Cysteine, Escherichia Coli, Lyases, Mercury, Diethyllead, Lyase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Wahba, M. J. Stevenson, A. Mansour, J. Sygusch, D. E. Wilcox, J. G. Omichinski
Structural And Biochemical Characterization Of Organotin An Organolead Compounds Binding To The Organomercurial Lyase Merb Provide New Insights Into Its Mechanism Of Carbon-Meta Bond Cleavage.
J. Am. Chem. Soc. V. 139 910 2017
PubMed-ID: 27989130  |  Reference-DOI: 10.1021/JACS.6B11327

(-) Compounds

Molecule 1 - ALKYLMERCURY LYASE
    Chains: A, B
    EC Number: 4.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BR1Ligand/IonBROMIDE ION
3ZN72Ligand/IonDIETHYLLEAD DIBROMIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BR-1Ligand/IonBROMIDE ION
3ZN71Ligand/IonDIETHYLLEAD DIBROMIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BR-1Ligand/IonBROMIDE ION
3ZN71Ligand/IonDIETHYLLEAD DIBROMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:96 , ASP A:99 , CYS A:159binding site for residue ZN7 A 301
2AC2SOFTWARELYS A:2binding site for residue BR A 302
3AC3SOFTWARECYS A:160 , HIS A:161 , HIS A:163 , TRP A:174 , HIS A:178 , HOH A:493 , HOH A:500binding site for residue ACT A 303
4AC4SOFTWARECYS B:96 , ASP B:99 , CYS B:159binding site for residue ZN7 B 301
5AC5SOFTWAREHOH A:429 , CYS B:160 , HIS B:161 , HIS B:163 , TRP B:174 , HIS B:178 , HOH B:427 , HOH B:504binding site for residue ACT B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U7C)

(-) 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 5U7C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U7C)

(-) Exons   (0, 0)

(no "Exon" information available for 5U7C)

(-) 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
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh...ee.....eee..ee.....eeeee..eeeee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee.......hhhhhhhhhh.ee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7c 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh...ee.....eee..ee.....eeeee..eeeee.hhhhhhhhhhhhh..eeeeee......eeeeee....eeeee....eeee.......hhhhhhhhhh.ee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7c B   1 MKLAPYILELLTSVNRTNGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMS 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 5U7C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U7C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U7C)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  5u7c
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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 3f2h 3fn8 5c0t 5c0u 5dsf 5u79 5u7a 5u7b 5u82 5u83 5u88

(-) Related Entries Specified in the PDB File

3f0p 3F0P IS MERB
5c17
5u79
5u7a
5u7b
5u82
5u83
5u88