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PR00946

Identifier
HGSCAVENGER  [View Relations]  [View Alignment]  
Accession
PR00946
No. of Motifs
6
Creation Date
24-JUL-1998  (UPDATE 07-JUN-1999)
Title
Mercury scavenger protein signature
Database References

PROSITE; PS01047 HMA
BLOCKS; BL01047
INTERPRO; IPR001802
PDB; 1AFI; 1AFJ
SCOP; 1AFI; 1AFJ
Literature References
1. BULL, P.C. AND COX, D.W. 
Wilson disease and Menkes disease - new handles on heavy-metal transport.
TRENDS GENET. 10 246-252 (1994).
 
2. STEELE, R.A. AND OPELLA, S.J.
Structures of the reduced and mercury-bound forms of MerP, the periplasmic
protein from the bacterial mercury detoxification system. 
BIOCHEMISTRY 36 6885-6895 (1997). 

Documentation
Proteins that transport heavy metals in micro-organisms and mammals share
similarities in their sequences and structures. These proteins provide an
important focus for research, some being involved in bacterial resistance
to toxic metals, such as lead and cadmium, while others are involved in
inherited human syndromes, such as Wilson and Menkes diseases [1].
 
A conserved 30-residue domain has been found in a number of these heavy
metal transport or detoxification proteins [1]. The domain, which has been
termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that
are probably involved in metal binding. 
 
The HMA domain has been identified in the N-terminal regions of a variety
of cation transporting ATPases, and in other ATPases such as fixI from 
Rhizobium meliloti; pacS from Synechococcus strain PCC 7942; Mycobacterium 
leprae ctpA and ctpB; and Escherichia coli hypothetical protein yhhO. In
addition, the domain has been found in bacterial mercuric reductase; the
copP copper-binding protein of Helicobacter pylori; and in the N-terminal 
regions of mercuric transport protein periplasmic component (gene merP) and
plasmids carried by mercury-resistant Gram-negative bacteria, where it seems
to be a mercury scavenger that specifically binds to one Hg(2+) ion, passing
this to mercuric reductase via the merT protein. 
 
The structure of the mercuric ion-binding protein MerP from Shigella
flexneri has been determined. The fold has been classed as a ferredoxin-like
alpha-beta sandwich, having a beta-alpha beta-beta alpha-beta architecture,
with the two alpha-helices overlaying a four-stranded anti-parallel beta-
sheet [2]. Structural differences between the reduced and mercury-bound 
forms of merP are localised to the metal-binding loop containing the 
consensus sequence GMTCXXC, the two cysteines of which are involved in
bi-coordination of Hg(2+) [2].
 
HGSCAVENGER is a 6-element fingerprint that provides a signature for
mercury scavenger proteins. The fingerprint was derived from an initial
alignment of 8 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length - motif 1 lies at the N-
terminus and spans the signal sequence; motifs 2-4 span the heavy-metal 
binding domain, and include the region encoded by PROSITE pattern HMA 
(PS01047), within which the two Cys residues are involved in metal binding
(motif 2 encodes the first beta-strand, motif 3 includes the first alpha-
helix and motif 4 spans strand 2); and motifs 5 and 6 lie towards the C-
terminus, motif 5 including strand 3, and motif 6 spanning helix 2 and 
strand 4. Two iterations on OWL30.2 were required to reach convergence, 
at which point a true set comprising 11 sequences was identified. Several
partial matches were also found, all of which are fragments, or closely-
related class II mercury-binding proteins.
 
 
An update on SPTR37_9f identified a true set of 12 sequences, and 3
partial matches.
Summary Information
  12 codes involving  6 elements
1 codes involving 5 elements
1 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
6121212121212
5011111
4011101
3000000
2001001
123456
True Positives
MERP_ACICA    MERP_ALCSP    MERP_ENTAG    MERP_PSEAE    
MERP_PSEFL MERP_SERMA MERP_SHIFL O05608
O07301 O66016 O66047 Q56445
True Positive Partials
Codes involving 5 elements
MERP_SHEPU
Codes involving 4 elements
O68532
Codes involving 2 elements
O54318
Sequence Titles
MERP_ACICA  MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - ACINETOBACTER CALCOACETICUS. 
MERP_ALCSP MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - ALCALIGENES SP.
MERP_ENTAG MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - ENTEROBACTER AGGLOMERANS, AND ENTEROBACTER CLOACAE.
MERP_PSEAE MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - PSEUDOMONAS AERUGINOSA.
MERP_PSEFL MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - PSEUDOMONAS FLUORESCENS.
MERP_SERMA MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - SERRATIA MARCESCENS.
MERP_SHIFL MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - SHIGELLA FLEXNERI.
O05608 PERIPLASMIC MERCURIC ION BINDING PROTEIN - PSEUDOMONAS SP.
O07301 MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - PSEUDOMONAS SP.
O66016 MERP - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
O66047 MERCURY TRANSPORT PROTEIN - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
Q56445 MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - UNIDENTIFIED.

MERP_SHEPU MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR (PERIPLASMIC MERCURY ION BINDING PROTEIN) (MERCURY SCAVENGER PROTEIN) - SHEWANELLA PUTREFACIENS (PSEUDOMONAS PUTREFACIENS).

O68532 MERCURIC ION TRANSPORT PROTEIN HOMOLOG - PSEUDOMONAS ALCALIGENES.

O54318 PERIPLASMIC TRANSPORT PROTEIN MER P - THIOBACILLUS SP.
Scan History
OWL30_2    2  100  NSINGLE    
SPTR37_9f 2 45 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
KKLFAALALAAVVAPVWAA MERP_ALCSP 2 2 -
KKLLSALALAAVVAPVWAA MERP_PSEFL 2 2 -
KKLFASLALAAAVAPVWAA MERP_SHIFL 2 2 -
KKLFAALALAAVVAPVWAA MERP_ENTAG 2 2 -
KKLFASLALAAFVAPVFAA MERP_ACICA 2 2 -
KTLALMSLFVLTSLNALAA MERP_PSEPT 2 2 -
KKLFASLALAAVVAPVWAA MERP_PSEAE 2 2 -
KKLFASLAIAAVVAPVWAA MERP_SERMA 2 2 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ATQTVTLSVPGM MERP_ALCSP 20 -1 -
ATQTVTLAVPGM MERP_SHIFL 20 -1 -
APKTVTLEVPTM MERP_PSEPT 20 -1 -
ATQTVTLSVPGM MERP_ACICA 20 -1 -
ATQTVTLSVPGM MERP_ENTAG 20 -1 -
ATQTVTLSVPGM MERP_PSEAE 20 -1 -
ATQTVTLSVPGM MERP_SERMA 20 -1 -
ATQTVTLSVPGM MERP_PSEFL 20 -1 -

Motif 3 width=17
Element Seqn Id St Int Rpt
MTCAACPITVKKALSKV MERP_SHIFL 31 -1 -
MNCVTCPFTVEKALQKV MERP_PSEPT 31 -1 -
MTCSACPITVKKAISEV MERP_PSEAE 31 -1 -
MTCSACPITVKKAISKV MERP_SERMA 31 -1 -
MTCSTCPITVKKAISKV MERP_ALCSP 31 -1 -
MTCSACPITVKKAISKV MERP_PSEFL 31 -1 -
MTCASCPITVKHALSKV MERP_ENTAG 31 -1 -
MTCASCPITVKHALSKV MERP_ACICA 31 -1 -

Motif 4 width=16
Element Seqn Id St Int Rpt
VEGVSKTDVSFDKRQA MERP_ENTAG 47 -1 -
VDGVSKAEVTFKTKLA MERP_PSEPT 47 -1 -
VEGVSKTDVSFDKRQA MERP_ACICA 47 -1 -
VEGVSKVDVTFETRQA MERP_PSEAE 47 -1 -
VEGVSKVNVTFETREA MERP_SERMA 47 -1 -
VEGVSKIDVTFETREA MERP_ALCSP 47 -1 -
VDGVSKVDVTFETREA MERP_PSEFL 47 -1 -
VEGVSKVDVGFEKREA MERP_SHIFL 47 -1 -

Motif 5 width=15
Element Seqn Id St Int Rpt
AVVTFDDAKTSVQKL MERP_ALCSP 62 -1 -
AVVTFDDAKTSVQKL MERP_PSEAE 62 -1 -
AVVTFDDAKTSVQKL MERP_SERMA 62 -1 -
AVVTFDDAKTSVQKL MERP_PSEFL 62 -1 -
AVVTFDDTKASVQKL MERP_SHIFL 62 -1 -
AVVTFDDAKTNVQKL MERP_ENTAG 62 -1 -
AVVTFDDAKTNVQKL MERP_ACICA 62 -1 -
AVVTFDDEKSTVKAL MERP_PSEPT 62 -1 -

Motif 6 width=15
Element Seqn Id St Int Rpt
LTKATEDAGYPSSVK MERP_PSEFL 76 -1 -
LTKATEDAGYPSSLK MERP_ACICA 76 -1 -
LTKATADAGYPSSVK MERP_PSEAE 76 -1 -
LTEATTNAGYPSTLK MERP_PSEPT 76 -1 -
LTKATEDAGYPSSLK MERP_ENTAG 76 -1 -
LTKATADAGYPSSVK MERP_SHIFL 76 -1 -
LTKATEDAGYPSSVK MERP_SERMA 76 -1 -
LTKATGDAGYPSSVK MERP_ALCSP 76 -1 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
KKLFASLALAAVVAPVWAA O66016 2 2 -
KKLFASLALAAVVAPVWAA MERP_PSEAE 2 2 -
KKLFASLAIAAVVAPVWAA MERP_SERMA 2 2 -
KKLFAALALAAVVAPVWAA MERP_ALCSP 2 2 -
KKLLSALALAAVVAPVWAA MERP_PSEFL 2 2 -
KKLLSALALAAVVAPVWAA Q56445 2 2 -
KKLFASLALAAAVAPVWAA MERP_SHIFL 2 2 -
KKLFASLLLAAAIVPAWAA O66047 2 2 -
KKLFAALALAAVVAPVWAA MERP_ENTAG 2 2 -
KKLFASLALAAFVAPVFAA MERP_ACICA 2 2 -
KKLFASLALAAAVAPVWAA O07301 2 2 -
RKLLASLALASLVATPVWA O05608 2 2 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ATQTVTLSVPGM O66016 20 -1 -
ATQTVTLSVPGM MERP_PSEAE 20 -1 -
ATQTVTLSVPGM MERP_SERMA 20 -1 -
ATQTVTLSVPGM MERP_ALCSP 20 -1 -
ATQTVTLSVPGM MERP_PSEFL 20 -1 -
ATQTVTLSVPGM Q56445 20 -1 -
ATQTVTLAVPGM MERP_SHIFL 20 -1 -
AVQTVTLSVPGM O66047 20 -1 -
ATQTVTLSVPGM MERP_ENTAG 20 -1 -
ATQTVTLSVPGM MERP_ACICA 20 -1 -
ATQTVTLAVPGM O07301 20 -1 -
ATQTVTLAVPGM O05608 21 0 -

Motif 3 width=17
Element Seqn Id St Int Rpt
MTCSACPITVKKAISKV O66016 31 -1 -
MTCSACPITVKKAISEV MERP_PSEAE 31 -1 -
MTCSACPITVKKAISKV MERP_SERMA 31 -1 -
MTCSTCPITVKKAISKV MERP_ALCSP 31 -1 -
MTCSACPITVKKAISKV MERP_PSEFL 31 -1 -
MTCSACPITVKKAISKV Q56445 31 -1 -
MTCAACPITVKKALSKV MERP_SHIFL 31 -1 -
MTCAACPITVKKAISKV O66047 31 -1 -
MTCASCPITVKHALSKV MERP_ENTAG 31 -1 -
MTCASCPITVKHALSKV MERP_ACICA 31 -1 -
MTCATCPITIKKALSKV O07301 31 -1 -
MTCAACPITVKTALTKV O05608 32 -1 -

Motif 4 width=16
Element Seqn Id St Int Rpt
VEGVSKVDVTFETRQA O66016 47 -1 -
VEGVSKVDVTFETRQA MERP_PSEAE 47 -1 -
VEGVSKVNVTFETREA MERP_SERMA 47 -1 -
VEGVSKIDVTFETREA MERP_ALCSP 47 -1 -
VDGVSKVDVTFETREA MERP_PSEFL 47 -1 -
VDGVSKVDVTFETREA Q56445 47 -1 -
VEGVSKVDVGFEKREA MERP_SHIFL 47 -1 -
VEGVSKVDVTFETREA O66047 47 -1 -
VEGVSKTDVSFDKRQA MERP_ENTAG 47 -1 -
VEGVSKTDVSFDKRQA MERP_ACICA 47 -1 -
VDGVSKTEVDFSTKLA O07301 47 -1 -
VDGVTKAEVSFENREA O05608 48 -1 -

Motif 5 width=15
Element Seqn Id St Int Rpt
AVVTFDDAKTSVQKL O66016 62 -1 -
AVVTFDDAKTSVQKL MERP_PSEAE 62 -1 -
AVVTFDDAKTSVQKL MERP_SERMA 62 -1 -
AVVTFDDAKTSVQKL MERP_ALCSP 62 -1 -
AVVTFDDAKTSVQKL MERP_PSEFL 62 -1 -
AVVTFDDAKTSVQKL Q56445 62 -1 -
AVVTFDDTKASVQKL MERP_SHIFL 62 -1 -
AVVTFDDAKTSVQKL O66047 62 -1 -
AVVTFDDAKTNVQKL MERP_ENTAG 62 -1 -
AVVTFDDAKTNVQKL MERP_ACICA 62 -1 -
AVVTFDDAKTNVQAL O07301 62 -1 -
AIVTFDDTKTNALAL O05608 63 -1 -

Motif 6 width=15
Element Seqn Id St Int Rpt
LTKATADAGYPSSVK O66016 76 -1 -
LTKATADAGYPSSVK MERP_PSEAE 76 -1 -
LTKATEDAGYPSSVK MERP_SERMA 76 -1 -
LTKATGDAGYPSSVK MERP_ALCSP 76 -1 -
LTKATEDAGYPSSVK MERP_PSEFL 76 -1 -
LTKATEDAGYPSSVK Q56445 76 -1 -
LTKATADAGYPSSVK MERP_SHIFL 76 -1 -
LTKATGDAGYPSSVK O66047 76 -1 -
LTKATEDAGYPSSLK MERP_ENTAG 76 -1 -
LTKATEDAGYPSSLK MERP_ACICA 76 -1 -
LSKATTDVGYPSELK O07301 76 -1 -
LTKATEDAGYPSSVK O05608 77 -1 -