3F2F - JenaLib

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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 :   29 Oct 08 (Deposition) - 11 Nov 08 (Release) - 20 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	BR	1	Ligand/Ion	BROMIDE ION
2	HG	2	Ligand/Ion	MERCURY (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:96 , ASP A:99 , CYS A:159 , HOH A:312	BINDING SITE FOR RESIDUE HG A 213
2	AC2	SOFTWARE	CYS B:96 , ASP B:99 , CYS B:159 , HOH B:220	BINDING SITE FOR RESIDUE HG B 213
3	AC3	SOFTWARE	HOH B:315	BINDING SITE FOR RESIDUE BR B 214

(no "SS Bond" information available for 3F2F)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3F2F)

(no "PROSITE Motif" information available for 3F2F)

(no "Exon" information available for 3F2F)

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 d3f2fa1 A:1-80 Alkylmercury lyase MerB                                          d3f2fa2 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.hhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f2f 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:197
 aligned with MERB_ECOLX | P77072 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
           MERB_ECOLX     1 MKLAPYILELLTSVNRTNGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQ 205
               SCOP domains d3f2fb1 B:1-8     0 Alkylmercury lyase MerB                                     d3f2fb2 B:81-205 Alkylmercury lyase MerB                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh-----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
                 3f2f B   1 MKLAPYILELLTS-----GTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLP---ADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQ 205
                                    10  |     20        30        40        50        60        70        80        90       100       110       120       130       140       | - |     160       170       180       190       200     
                                       13    19                                                                                                                              148 152

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: MerB N-terminal domain-like (7)

Protein domain: Alkylmercury lyase MerB (7)

Escherichia coli [TaxId: 562] (7)

1a	d3f2fa1	A:1-80
1b	d3f2fb1	B:1-80

Class: Alpha and beta proteins (a+b) (23004)

Fold: NosL/MerB-like (9)

Superfamily: NosL/MerB-like (9)

Family: MerB-like (7)

Protein domain: Alkylmercury lyase MerB (7)

Escherichia coli [TaxId: 562] (7)

2a	d3f2fa2	A:81-208
2b	d3f2fb2	B:81-205

(no "CATH Domain" information available for 3F2F)

(no "Pfam Domain" information available for 3F2F)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:137 - Pro A:138	[ RasMol ]
		Glu B:137 - Pro B:138	[ RasMol ]

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1s6l	NMR SOLUTION STRUCTURE OF THE SAME PROTEIN
3f0o	CRYSTAL STRUCTURE OF THE FREE FORM
3f0p	SIMILAR STRUCTURE OF THE MERCURY-BOUND FORM, PRODUCED BY DIFFERENT EXPERIMENTAL CONDITIONS
3f2g
3f2h

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