{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: prosite@expasy.org

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 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 license@isb-sib.ch 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 license@isb-sib.ch 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 license@isb-sib.ch 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 license@isb-sib.ch or
see: http://www.expasy.org/prosite/prosite_license.htm.
+------------------------------------------------------------------------+

{END}
{PDOC60030}
{PS60030; BACTERIOCIN_IIA}
{BEGIN}
******************************************
* Bacteriocin class IIa family signature *
******************************************

Many Gram-positive  bacteria  produce  ribosomally  synthesized  antimicrobial
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 food-associated
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 C-terminal
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  known  to belong to the class IIa bacteriocin family are listed
below:

 - 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  for  the  class  IIa bacteriocin family covers the
'pediocin box' motif.

-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.; ramak@physics.iisc.ernet.in

-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 license@isb-sib.ch or
see: http://www.expasy.org/prosite/prosite_license.htm.
+------------------------------------------------------------------------+

{END}