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PR01595

Identifier
SYCDCHAPRONE  [View Relations]  [View Alignment]  
Accession
PR01595
No. of Motifs
4
Creation Date
22-SEP-2001
Title
Gram-negative bacterial type III secretion SycD chaperone signature
Database References
Literature References
1. HUECK, C.J.
Type III protein secretion systems in bacterial pathogens of animals and 
plants.
MICROBIOL.MOL.BIOL.REV. 379-433 (1998). 
 
2. WILLIAMS, A.W. AND STRALEY, S.C. 
YopD of Yersinia pestis plays a role in negative regulation of the low-
calcium response in addition to its role in translocation of Yops.
J.BACTERIOL. 180 350-358 (1998).
 
3. WATTIAU, P., BERNIER, B., DESLEE, P., MICHIELS, T. AND CORNELIS, G.R.
Individual chaperones required for Yop secretion by Yersinia.
PROC.NATL.ACAD.SCI.U.S.A. 91 10493-10497 (1994).
 
4. NEYT, C. AND CORNELIS, G.R.
Role of SycD, the chaperone of the Yersinia Yop translocators YopB and YopD.
MOL.MICROBIOL. 31 143-156 (1999).
 
5. FIELDS, K.A. AND HACKSTADT, T. 
Evidence for the secretion of Chlamydia trachomatis CopN by a type III
secretion mechanism.
MOL.MICROBIOL. 38 1048-1060 (2000).

Documentation
Secretion of virulence factors in Gram-negative bacteria involves 
transportation of the protein across two membranes to reach the cell 
exterior [1]. There have been four secretion systems described in 
animal enteropathogens, such as Salmonella and Yersinia, with further 
sequence similarities in plant pathogens like Ralstonia and Erwinia [1]. 
 
The type III secretion system is of great interest, as it is used to 
transport virulence factors from the pathogen directly into the host cell 
[1] and is only triggered when the bacterium comes into close contact with
the host. The protein subunits of the system are very similar to those of 
bacterial flagellar biosynthesis [1]. However, while the latter forms a
ring structure to allow secretion of flagellin and is an integral part of
the flagellum itself [1], type III subunits in the outer membrane 
translocate secreted proteins through a channel-like structure.
 
Effector proteins secreted by the type III system do not possess a secretion 
signal, and are considered unique because of this [1]. Yersinia spp. secrete 
effector proteins called YopB and YopD through the type III needle [2]. Both 
are believed to act as pore translocases, forming apertures in the host cell 
membrane and allowing the bacterium easy access to its cytoplasm [2,3]. YopD
also acts as a negative regulator of the Yersinia low-calcium response, and 
in turn is controlled by a chaperone, SycD [3]. This protein also regulates
YopB secretion. SycD is located on the Yop pathogenicity island of Yersinia 
spp., and is speculated to prevent a premature interaction between YopB, 
YopD and the calcium-response LcrV protein [4]. 
 
It has been speculated that a type III secretion mechanism also exists in
Chlamydial species. With the sequencing of the Chlamydia trachomatis genome,
several proteins similar to characterised type III proteins have emerged, 
including a SycD homologue [5]. The Pseudomonas aeruginosa gene PcrH is also 
similar to the Yersinia chaperone, suggesting a comparable function.
 
SYCDCHAPRONE is a 4-element fingerprint that provides a signature for the
Gram-negative bacterial type III secretion SycD chaperone protein family.
The fingerprint was derived from an initial alignment of 7 sequences: the
motifs were drawn from conserved regions spanning virtually the full
alignment length. Two iterations on SPTR39_17f were required to reach
convergence, at which point a true set comprising 8 sequences was identified.
Several partial matches were also found: those matching 3 motifs include a
Chlamydial type III secretion chaperone and a low calcium response protein,
which fail to make signficant matches with motif 2; those that match 2
motifs include invasion and pathogenicity proteins from Shigella
dysenteriae, Thermoplasma acidophilum and Escherichia coli.
Summary Information
   8 codes involving  4 elements
2 codes involving 3 elements
4 codes involving 2 elements
Composite Feature Index
48888
32022
23320
1234
True Positives
LCRH_YERPE    LCRH_YERPS    O30528        O84580        
O87496 Q9I325 Q9PJG4 Q9Z795
True Positive Partials
Codes involving 3 elements
O84870 Q9PL56
Codes involving 2 elements
IPPI_SHIFL O52134 Q9AJ22 Q9HM31
Sequence Titles
LCRH_YERPE  LOW CALCIUM RESPONSE LOCUS PROTEIN H - Yersinia pestis. 
LCRH_YERPS LOW CALCIUM RESPONSE LOCUS PROTEIN H - Yersinia pseudotuberculosis.
O30528 PCRH - Pseudomonas aeruginosa.
O84580 LOW CALCIUM RESPONSE PROTEIN H - Chlamydia trachomatis.
O87496 SYCD PROTEIN - Yersinia enterocolitica.
Q9I325 REGULATORY PROTEIN PCRH - Pseudomonas aeruginosa.
Q9PJG4 TYPE III SECRETION CHAPERONE SYCD - Chlamydia muridarum.
Q9Z795 LOW CALCIUM RESPONSE PROTEIN H - Chlamydia pneumoniae (Chlamydophila pneumoniae).

O84870 LOW CALCIUM RESPONSE PROTEIN H - Chlamydia trachomatis.
Q9PL56 TYPE III SECRETION CHAPERONE - Chlamydia muridarum.

IPPI_SHIFL IPPI PROTEIN - Shigella flexneri, and Shigella dysenteriae.
O52134 CESD - Escherichia coli.
Q9AJ22 CESD - Escherichia coli.
Q9HM31 72K MITOCHONDRIAL OUTER MEMBRANE PROTEIN RELATED PROTEIN - Thermoplasma acidophilum.
Scan History
SPTR39.22_17.3f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=24
Element Seqn Id St Int Rpt
GGTIAMLNEISSDTLEQLYSLAFN LCRH_YERPE 22 22 -
GGTIAMLNEISSDTLEQLYSLAFN O87496 22 22 -
GGTIAMLNEISSDTLEQLYSLAFN LCRH_YERPS 22 22 -
GGTLAMLRGLSEDTLEQLYALGFN O30528 23 23 -
GGTLAMLRGLSEDTLEQLYALGFN Q9I325 22 22 -
GLTLQQILGLSDVLLEEIYTVAYT Q9PJG4 79 79 -
GLTLQQILGLSDVLLEEIYTVAYT O84580 64 64 -

Motif 2 width=20
Element Seqn Id St Int Rpt
YSQGKYQEAIGLFQILTASK O84580 89 1 -
YQSGKYEDAHKVFQALCVLD LCRH_YERPE 47 1 -
YQSGKYEDAHKVFQALCVLD O87496 47 1 -
YQSGKYEDAHKVFQALCVLD LCRH_YERPS 47 1 -
YQAGKWDDAQKIFQALCMLD O30528 48 1 -
YQAGKWDDAQKIFQALCMLD Q9I325 47 1 -
YSQGKYREAIGLFQILTASK Q9PJG4 104 1 -

Motif 3 width=23
Element Seqn Id St Int Rpt
RFFLGLGACRQAMGQYDLAIHSY LCRH_YERPE 71 4 -
RFFLGLGACRQAMGQYDLAIHSY O87496 71 4 -
RFFLGLGACRQAMGQYDLAIHSY LCRH_YERPS 71 4 -
RYFLGLGACRQSLGLYEQALQSY O30528 72 4 -
RYFLGLGACRQSLGLYEQALQSY Q9I325 71 4 -
KYILGLSSCYHQLKMYDEAAFGF Q9PJG4 128 4 -
KYILGLSSCYHQLKMYDEAAFGF O84580 113 4 -

Motif 4 width=23
Element Seqn Id St Int Rpt
EPRFPFHAAECLLQKGELAEAES LCRH_YERPE 103 9 -
EPRFPFHAAECLLQKGELAEAES O87496 103 9 -
EPRFPFHAAECLLQKGELAEAES LCRH_YERPS 103 9 -
EPRFPFHAAECHLQLGDLDGAES O30528 104 9 -
EPRFPFHAAECHLQLGDLDGAES Q9I325 103 9 -
NPIPPYYIADSLMQLDQPEESQN Q9PJG4 160 9 -
NPIPPYYIADSLMKLNQPEESQD O84580 145 9 -
Final Motifs
Motif 1  width=24
Element Seqn Id St Int Rpt
GGTIAMLNEISSDTLEQLYSLAFN LCRH_YERPE 22 22 -
GGTIAMLNEISSDTLEQLYSLAFN O87496 22 22 -
GGTIAMLNEISSDTLEQLYSLAFN LCRH_YERPS 22 22 -
GGTLAMLRGLSEDTLEQLYALGFN O30528 23 23 -
GGTLAMLRGLSEDTLEQLYALGFN Q9I325 22 22 -
GLTLQQILGLSDVLLEEIYTVAYT Q9PJG4 79 79 -
GLTLQQILGLSDVLLEEIYTVAYT O84580 64 64 -
GLDLQQILGLSDYLLEEIYTVAYT Q9Z795 67 67 -

Motif 2 width=20
Element Seqn Id St Int Rpt
YSQGKYNEAVGLFQLLAAAQ Q9Z795 92 1 -
YQSGKYEDAHKVFQALCVLD LCRH_YERPE 47 1 -
YQSGKYEDAHKVFQALCVLD O87496 47 1 -
YQSGKYEDAHKVFQALCVLD LCRH_YERPS 47 1 -
YQAGKWDDAQKIFQALCMLD O30528 48 1 -
YQAGKWDDAQKIFQALCMLD Q9I325 47 1 -
YSQGKYREAIGLFQILTASK Q9PJG4 104 1 -
YSQGKYQEAIGLFQILTASK O84580 89 1 -

Motif 3 width=23
Element Seqn Id St Int Rpt
RFFLGLGACRQAMGQYDLAIHSY LCRH_YERPE 71 4 -
RFFLGLGACRQAMGQYDLAIHSY O87496 71 4 -
RFFLGLGACRQAMGQYDLAIHSY LCRH_YERPS 71 4 -
RYFLGLGACRQSLGLYEQALQSY O30528 72 4 -
RYFLGLGACRQSLGLYEQALQSY Q9I325 71 4 -
KYILGLSSCYHQLKMYDEAAFGF Q9PJG4 128 4 -
KYILGLSSCYHQLKMYDEAAFGF O84580 113 4 -
KYMLGLSSCYHQLHLYNEAAFGF Q9Z795 116 4 -

Motif 4 width=23
Element Seqn Id St Int Rpt
EPRFPFHAAECLLQKGELAEAES LCRH_YERPE 103 9 -
EPRFPFHAAECLLQKGELAEAES O87496 103 9 -
EPRFPFHAAECLLQKGELAEAES LCRH_YERPS 103 9 -
EPRFPFHAAECHLQLGDLDGAES O30528 104 9 -
EPRFPFHAAECHLQLGDLDGAES Q9I325 103 9 -
NPIPPYYIADSLMQLDQPEESQN Q9PJG4 160 9 -
NPIPPYYIADSLMKLNQPEESQD O84580 145 9 -
NPIPPYYIADSLLKLQQPEESNN Q9Z795 148 9 -