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PR01594

Identifier
SECBCHAPRONE  [View Relations]  [View Alignment]  
Accession
PR01594
No. of Motifs
4
Creation Date
06-SEP-2001
Title
Bacterial protein-transport SecB chaperone protein signature
Database References

PFAM; PF02556 Preprotein
INTERPRO; IPR003708
PDB; 1FX3
SCOP; 1FX3
CATH; 1FX3
Literature References
1. BIEKER, K.L., PHILLIPS, G.J. AND SILHAVY, T.J. 
The sec and prl genes of Esherichia coli.
J.BIOENERG.BIOMEMBR. 22 291-310 (1990). 
 
2. DRIESSEN, A.J.M.
SecB, a molecular chaperone with two faces
TRENDS MICROBIOL. 9 193-196 (2001).
 
3. MULLER, J.P.
Influence of impaired chaperone or secretion function on SecB production in gr; Escherichia coli.
J.BACTERIOL. 178 6097-6104 (1996). 
 
4. XU, Z., KNAFELS, J.D. AND YOSHINO, K.
Crystal structure of the bacterial protein export chaperone SEcB
NAT.STRUCT.BIOL. 7 1172-1177 (2000).

Documentation
Secretion across the inner membrane in some Gram-negative bacteria occurs
via the preprotein translocase pathway. Proteins are produced in the 
cytoplasm as precursors, and require a chaperone subunit to direct them to 
the translocase component. [1]. From there, the mature proteins are either 
targeted to the outer membrane, or remain as periplasmic proteins [1]. The 
translocase protein subunits are encoded on the bacterial chromosome.
 
The translocase itself comprises 7 proteins, including a chaperone protein
(SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and 
SecG), and two additional membrane proteins that promote the release of 
the mature peptide into the periplasm (SecD and SecF) [1]. The chaperone 
protein SecB [2] is a highly acidic homotetrameric protein that exists
as a "dimer of dimers" in the bacterial cytoplasm [2]. SecB maintains 
preproteins in an unfolded state after translation, and targets these to 
the peripheral membrane protein ATPase SecA for secretion [3].
 
Recently, the tertiary structure of Haemophilus influenzae SecB was resolved
by means of X-ray crystallography to 2.5A [4]. The chaperone comprises four
chains, forming a tetramer, each chain of which has a simple alpha+beta fold
arrangement. While one binding site on the homotetramer recognises unfolded
polypeptides by hydrophobic interactions, the second binds to SecA through
the latter's C-terminal 22 residues [4].
 
SECBCHAPRONE is a 4-element fingerprint that provides a signature for the
bacterial protein-transport SecB chaperone protein family. The fingerprint
was derived from an initial alignment of 4 sequences: the motifs were drawn
from conserved regions spanning virtually the full alignment length - motif
1 spans beta-strand 1 and the N-terminus of alpha-helix 1; motif 2 spans
strand 4 and the N-terminus of helix 2; motif 3 encompasses the C-terminus
of helix 2 and helix 3; and motif 4 spans most of helix 4. Three iterations
on SPTR39.22_17.3f were required to reach convergence, at which point a true
set comprising 13 sequences was identified.
Summary Information
13 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
413131313
30000
20000
1234
True Positives
Q9A224        Q9CL16        Q9EZ97        Q9HU56        
Q9JVU8 Q9JY16 Q9KNS8 Q9PCH8
SECB_BUCAI SECB_BUCAP SECB_ECOLI SECB_HAEIN
SECB_RICPR
Sequence Titles
Q9A224      PROTEIN-EXPORT PROTEIN SECB, PUTATIVE - Caulobacter crescentus. 
Q9CL16 SECB - Pasteurella multocida.
Q9EZ97 PROTEIN-EXPORT PROTEIN SECB (SECB) - Zymomonas mobilis.
Q9HU56 SECRETION PROTEIN SECB - Pseudomonas aeruginosa.
Q9JVU8 HYPOTHETICAL PROTEIN SECB OR NMA0674 - Neisseria meningitidis (serogroup A).
Q9JY16 PROTEIN-EXPORT PROTEIN SECB - Neisseria meningitidis (serogroup B).
Q9KNS8 PROTEIN-TRANSPORT PROTEIN SECB - Vibrio cholerae.
Q9PCH8 PROTEIN-EXPORT PROTEIN - Xylella fastidiosa.
SECB_BUCAI PROTEIN-EXPORT PROTEIN SECB - Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium).
SECB_BUCAP PROTEIN-EXPORT PROTEIN SECB - Buchnera aphidicola (subsp. Schizaphis graminum).
SECB_ECOLI PROTEIN-EXPORT PROTEIN SECB - Escherichia coli.
SECB_HAEIN PROTEIN-EXPORT PROTEIN SECB - Haemophilus influenzae.
SECB_RICPR PROTEIN-EXPORT PROTEIN SECB - Rickettsia prowazekii.
Scan History
SPTR39.22_17.3f 3  100  NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
IQRIYVKDVSFEAPNLPH SECB_HAEIN 20 20 -
IQRIYTKDISFEAPNAPH SECB_ECOLI 13 13 -
IQRIYIRDASFEAPNTPN SECB_BUCAP 13 13 -
VNAQYIKDLSLENPSAPS SECB_RICPR 17 17 -

Motif 2 width=21
Element Seqn Id St Int Rpt
AFICEVKQAGVFTISGLEDVQ SECB_HAEIN 82 44 -
AFLCEVQQGGIFSIAGIEGTQ SECB_ECOLI 73 42 -
VFLCDVHQVGIFFISCLDEQE SECB_BUCAP 73 42 -
LFQIELKYAGVFNLINIDSEQ SECB_RICPR 79 44 -

Motif 3 width=23
Element Seqn Id St Int Rpt
CLTSQCPNMLFPYARELVSNLVN SECB_HAEIN 106 3 -
CLGAYCPNILFPYARECITSMVS SECB_ECOLI 97 3 -
CLGSYCPNILFPYARTCISSLVS SECB_BUCAP 97 3 -
LLSVHCPAMIFPFARKIIASCTQ SECB_RICPR 103 3 -

Motif 4 width=19
Element Seqn Id St Int Rpt
FPALNLSPVNFDALFVEYM SECB_HAEIN 132 3 -
FPQLNLAPVNFDALFMNYL SECB_ECOLI 123 3 -
FPQLNLSPIDFDDIFCKNL SECB_BUCAP 123 3 -
FQPLMIDPIDFGALYHKKM SECB_RICPR 129 3 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
IQRIYVKDVSFEAPNLPH Q9CL16 22 22 -
IQRIYVKDVSFEAPNLPH SECB_HAEIN 20 20 -
IQRIYLKDVSFEAPSSPV Q9KNS8 14 14 -
IQRIYTKDISFEAPNAPH SECB_ECOLI 13 13 -
IQRIYIKDVSFEAPNTPN SECB_BUCAI 13 13 -
IQRIYIRDASFEAPNTPN SECB_BUCAP 13 13 -
LQRIYLRDLSFESPKSPE Q9HU56 19 19 -
IEKIYIKDVSFEAPNSPA Q9PCH8 40 40 -
IERLYVKDLSLEVPHAPQ Q9JVU8 11 11 -
IERLYVKDLSLEVPHAPQ Q9JY16 11 11 -
VNAQYIKDLSLENPSAPS SECB_RICPR 17 17 -
ILAQYIKDLSFENPNAPA Q9EZ97 21 21 -
ILAQFVRDFSFENPLAPD Q9A224 23 23 -

Motif 2 width=21
Element Seqn Id St Int Rpt
AFICEVKQAGVFTISGLEEMQ Q9CL16 84 44 -
AFICEVKQAGVFTISGLEDVQ SECB_HAEIN 82 44 -
AFLCEVQQAGIFSAEQMEAGQ Q9KNS8 74 42 -
AFLCEVQQGGIFSIAGIEGTQ SECB_ECOLI 73 42 -
VFLCDIDQAGIFFIANINEKR SECB_BUCAI 73 42 -
VFLCDVHQVGIFFISCLDEQE SECB_BUCAP 73 42 -
AFIAEVQQAGIFLIKNLDPSS Q9HU56 80 43 -
AYVVEVQQAGVFGLFGLDQHA Q9PCH8 100 42 -
MFLNEVTQSGIFRLENIPEED Q9JVU8 72 43 -
MFLNEVTQSGIFRLENIPEED Q9JY16 72 43 -
LFQIELKYAGVFNLINIDSEQ SECB_RICPR 79 44 -
VFHVELVYNGLFAIKNVPADQ Q9EZ97 81 42 -
VFHVEVVYGGLFHIAGIAEED Q9A224 84 43 -

Motif 3 width=23
Element Seqn Id St Int Rpt
CLTSQCPNMLFPYARELVSSLVN Q9CL16 108 3 -
CLTSQCPNMLFPYARELVSNLVN SECB_HAEIN 106 3 -
CLGAFCPNILFPYARETISSLVV Q9KNS8 98 3 -
CLGAYCPNILFPYARECITSMVS SECB_ECOLI 97 3 -
CLYSYCPNILFPYARTCISNLVS SECB_BUCAI 97 3 -
CLGSYCPNILFPYARTCISSLVS SECB_BUCAP 97 3 -
TLGAFCPNILFPYAREALDNLVV Q9HU56 104 3 -
LLGTQCPNILFPYVRSLVSDLIQ Q9PCH8 124 3 -
LLGVACPNILFPYAREAVSGTVT Q9JVU8 96 3 -
LLGVACPNILFPYAREAVSGTVT Q9JY16 96 3 -
LLSVHCPAMIFPFARKIIASCTQ SECB_RICPR 103 3 -
FLYIEAPRILFPFVRRILADSVR Q9EZ97 105 3 -
VLLIECPRFLFPYARRLISDVTA Q9A224 108 3 -

Motif 4 width=19
Element Seqn Id St Int Rpt
FPALNLSPVNFDALFMDYL Q9CL16 134 3 -
FPALNLSPVNFDALFVEYM SECB_HAEIN 132 3 -
FPQLNLAPVNFDALFMNYL Q9KNS8 124 3 -
FPQLNLAPVNFDALFMNYL SECB_ECOLI 123 3 -
FPQMNLAPINFDALYHDHI SECB_BUCAI 123 3 -
FPQLNLSPIDFDDIFCKNL SECB_BUCAP 123 3 -
FPALMLSPVNFDALYAQEI Q9HU56 130 3 -
FPPFYLQPINFDALYAETL Q9PCH8 150 3 -
FPPVLLAPINFEAIYQQQQ Q9JVU8 122 3 -
FPPVLLAPINFEAIYQQQQ Q9JY16 122 3 -
FQPLMIDPIDFGALYHKKM SECB_RICPR 129 3 -
FPPLMLEPIDFAALYMQQT Q9EZ97 131 3 -
FPPFLIDPIDFAGVYAARK Q9A224 134 3 -