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{PDOC00000}
{BEGIN}
**********************************
*** PROSITE documentation file ***
**********************************
Release 20.43 of 10-Feb-2009.
PROSITE is developed by the Swiss Institute of Bioinformatics (SIB) under
the responsability of Amos Bairoch and Nicolas Hulo.
This release was prepared by: Nicolas Hulo, Virginie Bulliard, Petra
Langendijk-Genevaux and Christian Sigrist with the help of Edouard
de Castro, Lorenzo Cerutti, Corinne Lachaize and Amos Bairoch.
See: http://www.expasy.org/prosite/
Email: [email protected]
Acknowledgements:
- To all those mentioned in this document who have reviewed the
entry(ies)
for which they are listed as experts. With specific thanks to Rein
Aasland,
Mark Boguski, Peer Bork, Josh Cherry, Andre Chollet, Frank Kolakowski,
David Landsman, Bernard Henrissat, Eugene Koonin, Steve Henikoff,
Manuel
Peitsch and Jonathan Reizer.
- Jim Apostolopoulos is the author of the PDOC00699 entry.
- Brigitte Boeckmann is the author of the PDOC00691, PDOC00703,
PDOC00829,
PDOC00796, PDOC00798, PDOC00799, PDOC00906, PDOC00907, PDOC00908,
PDOC00912, PDOC00913, PDOC00924, PDOC00928, PDOC00929, PDOC00955,
PDOC00961, PDOC00966, PDOC00988 and PDOC50020 entries.
- Jean-Louis Boulay is the author of the PDOC01051, PDOC01050,
PDOC01052,
PDOC01053 and PDOC01054 entries.
- Ryszard Brzezinski is the author of the PDOC60000 entry.
- Elisabeth Coudert is the author of the PDOC00373 entry.
- Kirill Degtyarenko is the author of the PDOC60001 entry.
- Christian Doerig is the author of the PDOC01049 entry.
- Kay Hofmann is the author of the PDOC50003, PDOC50006, PDOC50007 and
PDOC50017 entries.
- Chantal Hulo is the author of the PDOC00987 entry.
- Karine Michoud is the author of the PDOC01044 and PDOC01042 entries.
- Yuri Panchin is the author of the PDOC51013 entry.
- S. Ramakumar is the author of the PDOC51052, PDOC60004, PDOC60010,
PDOC60011, PDOC60015, PDOC60016, PDOC60018, PDOC60020, PDOC60021,
PDOC60022, PDOC60023, PDOC60024, PDOC60025, PDOC60026, PDOC60027,
PDOC60028, PDOC60029 and PDOC60030 entries.
- Keith Robison is the author of the PDOC00830 and PDOC00861 entries.
----------------------------------------------------------------------PROSITE is copyright.
It
is
produced
by
the
Swiss
Institute
of
Bioinformatics (SIB). There are no restrictions on its use by nonprofit
institutions as long as its content is in no way modified. Usage by
and
for commercial entities requires a license agreement.
For
information
about the licensing scheme
send an email to [email protected]
or
see: http://www.expasy.org/prosite/prosite_license.htm.
----------------------------------------------------------------------+-----------------------------------------------------------------------+
PROSITE is copyright.
It is produced by the Swiss Institute
of
Bioinformatics (SIB). There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and
for commercial entities requires a license agreement.
For information
about the licensing scheme
send an email to [email protected] or
see: http://www.expasy.org/prosite/prosite_license.htm.
+-----------------------------------------------------------------------+
{END}
{PDOC00001}
{PS00001; ASN_GLYCOSYLATION}
{BEGIN}
************************
* N-glycosylation site *
************************
It has been known for a long time [1] that potential N-glycosylation
sites are
specific to the consensus sequence Asn-Xaa-Ser/Thr. It must be noted
that the
presence of the consensus tripeptide is not sufficient to conclude
that an
asparagine residue is glycosylated, due to the fact that the folding of
the
protein plays an important role in the regulation of N-glycosylation
[2]. It
has been shown [3] that the presence of proline between Asn and Ser/Thr
will
inhibit N-glycosylation; this has been confirmed by a recent [4]
statistical
analysis of glycosylation sites, which also shows that about 50% of the
sites
that have a proline C-terminal to Ser/Thr are not glycosylated.
It must also be noted that there are a few reported cases of
glycosylation
sites with the pattern Asn-Xaa-Cys; an experimentally demonstrated
occurrence
of such a non-standard site is found in the plasma protein C [5].
-Consensus pattern: N-{P}-[ST]-{P}
[N is the glycosylation site]
-Last update: May 1991 / Text revised.
[ 1] Marshall R.D.
"Glycoproteins."
Annu. Rev. Biochem. 41:673-702(1972).
PubMed=4563441; DOI=10.1146/annurev.bi.41.070172.003325
[ 2] Pless D.D., Lennarz W.J.
"Enzymatic conversion of proteins to glycoproteins."
Proc. Natl. Acad. Sci. U.S.A. 74:134-138(1977).
PubMed=264667
[ 3] Bause E.
"Structural requirements of N-glycosylation of proteins. Studies
with
proline peptides as conformational probes."
Biochem. J. 209:331-336(1983).
PubMed=6847620
[ 4] Gavel Y., von Heijne G.
"Sequence differences between glycosylated and non-glycosylated
Asn-X-Thr/Ser acceptor sites: implications for protein engineering."
Protein Eng. 3:433-442(1990).
PubMed=2349213
[ 5] Miletich J.P., Broze G.J. Jr.
"Beta protein C is not glycosylated at asparagine 329. The rate of
translation may influence the frequency of usage at
asparagine-X-cysteine sites."
J. Biol. Chem. 265:11397-11404(1990).
PubMed=1694179
+-----------------------------------------------------------------------+
PROSITE is copyright.
It is produced by the Swiss Institute
of
Bioinformatics (SIB). There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and
for commercial entities requires a license agreement.
For information
about the licensing scheme
send an email to [email protected] or
see: http://www.expasy.org/prosite/prosite_license.htm.
+-----------------------------------------------------------------------+
{END}
{PDOC00004}
{PS00004; CAMP_PHOSPHO_SITE}
{BEGIN}
****************************************************************
* cAMP- and cGMP-dependent protein kinase phosphorylation site *
****************************************************************
There has been a number of studies relative to the specificity of
cAMP- and
cGMP-dependent protein kinases [1,2,3]. Both types of kinases appear to
share
a preference for the phosphorylation of serine or threonine residues
found
close to at least two consecutive N-terminal basic residues. It is
important
to note that there are quite a number of exceptions to this rule.
-Consensus pattern: [RK](2)-x-[ST]
[S or T is the phosphorylation site]
-Last update: June 1988 / First entry.
[ 1] Fremisco J.R., Glass D.B., Krebs E.G.
J. Biol. Chem. 255:4240-4245(1980).
[ 2] Glass D.B., Smith S.B.
"Phosphorylation by cyclic GMP-dependent protein kinase of a
synthetic
peptide corresponding to the autophosphorylation site in the
enzyme."
J. Biol. Chem. 258:14797-14803(1983).
PubMed=6317673
[ 3] Glass D.B., el-Maghrabi M.R., Pilkis S.J.
"Synthetic peptides corresponding to the site phosphorylated in
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase as substrates
of
cyclic nucleotide-dependent protein kinases."
J. Biol. Chem. 261:2987-2993(1986).
PubMed=3005275
+-----------------------------------------------------------------------+
PROSITE is copyright.
It is produced by the Swiss Institute
of
Bioinformatics (SIB). There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and
for commercial entities requires a license agreement.
For information
about the licensing scheme
send an email to [email protected] or
see: http://www.expasy.org/prosite/prosite_license.htm.
+-----------------------------------------------------------------------+
{END}
{PDOC60030}
{PS60030; BACTERIOCIN_IIA}
{BEGIN}
******************************************
* Bacteriocin class IIa family signature *
******************************************
Many Gram-positive
antimicrobial
bacteria
produce
ribosomally
synthesized
peptides, often termed bacteriocins. One important and well studied
class of
bacteriocins is the class IIa or pediocin-like bacteriocins produced by
lactic
acid bacteria. All class IIa bacteriocins are produced by foodassociated
strains, isolated from a variety of food products of industrial and
natural
origins, including meat products, dairy products and vegetables.
Class IIa
bacteriocins are all cationic, display anti-Listeria activity, and kill
target
cells by permeabilizing the cell membrane [1-3].
Class IIa bacteriocins contain between 37 and 48 residues. Based on
their
primary structures, the peptide chains of class IIa bacteriocins
may be
divided roughly into two regions: a hydrophilic, cationic and highly
conserved
N-terminal region, and a less conserved hydrophobic/amphiphilic Cterminal
region. The N-terminal region contains the conserved Y-G-N-G-V/L
'pediocin
box' motif and two conserved cysteine residues joined by a disulfide
bridge.
It forms a three-stranded antiparallel beta-sheet supported by the
conserved
disulfide bridge (see <PDB:1OG7>). This cationic N-terminal beta-sheet
domain
mediates binding of the class IIa bacteriocin to the target cell
membrane. The
C-terminal region forms a hairpin-like domain (see <PDB:1OG7>) that
penetrates
into the hydrophobic part of the target cell membrane, thereby
mediating
leakage through the membrane. The two domains are joined by a hinge,
which
enables movement of the domains relative to each other [2,3].
Some proteins
listed
below:
-
known
to belong to the class IIa bacteriocin family are
Pediococcus acidilactici pediocin PA-1.
Leuconostoc mesenteroides mesentericin Y105.
Carnobacterium piscicola carnobacteriocin B2.
Lactobacillus sake sakacin P.
Enterococcus faecium enterocin A.
Enterococcus faecium enterocin P.
Leuconostoc gelidum leucocin A.
Lactobacillus curvatus curvacin A.
Listeria innocua listeriocin 743A.
The pattern we developed
covers the
'pediocin box' motif.
for
the
class
IIa bacteriocin family
-Conserved pattern: Y-G-N-G-[VL]-x-C-x(4)-C
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Expert(s) to contact by email:
Ramakumar S.; [email protected]
-Last update: March 2006 / First entry.
[ 1] Ennahar S., Sonomoto K., Ishizaki A.
"Class IIa bacteriocins from lactic acid bacteria: antibacterial
activity and food preservation."
J. Biosci. Bioeng. 87:705-716(1999).
PubMed=16232543
[ 2] Johnsen L., Fimland G., Nissen-Meyer J.
"The C-terminal domain of pediocin-like antimicrobial peptides
(class
IIa bacteriocins) is involved in specific recognition of the
C-terminal part of cognate immunity proteins and in determining the
antimicrobial spectrum."
J. Biol. Chem. 280:9243-9250(2005).
PubMed=15611086; DOI=10.1074/jbc.M412712200
[ 3] Fimland G., Johnsen L., Dalhus B., Nissen-Meyer J.
"Pediocin-like antimicrobial peptides (class IIa bacteriocins) and
their immunity proteins: biosynthesis, structure, and mode of
action."
J. Pept. Sci. 11:688-696(2005).
PubMed=16059970; DOI=10.1002/psc.699
+-----------------------------------------------------------------------+
PROSITE is copyright.
It is produced by the Swiss Institute
of
Bioinformatics (SIB). There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and
for commercial entities requires a license agreement.
For information
about the licensing scheme
send an email to [email protected] or
see: http://www.expasy.org/prosite/prosite_license.htm.
+-----------------------------------------------------------------------+
{END}