Re: How does mitochondrial ATP synthase work?

X-Sender: kpmitton@pop.groupwise.med.umich.edu (Unverified)
Date: Wed, 01 Jul 1998 13:48:09 -0400
To: kpmitton@umich.edu
From: "Kenneth P. Mitton, Ph.D." 
Subject: atpsynthase
Mime-Version: 1.0

http://expasy.hcuge.ch/cgi-bin/prosite-search-de

is the Prosite search page at the expasy.hcuge.ch     
EXPASY server for molecular biology in Switzerland.
You can get to the expasy server also using our lab's home page

http://141.214.184.151/swaroop.html

I searched ATP and found the Prosite documents on domains, sequence
signatures etc for ATP sythetase.

You will find the expasy site to be very handy indeed. I have pasted two of 
several documents available, you will find links to others describing the 
other subunits of the synthetase. These documents are nice because they are 
updated and they provide journal references to the information.

The Prosite database is very useful for gathering domain/function 
information quickly on any proteins where such information is known in the 
literature. Go to the Prosite database at Expasy and you can use the 
prosite document numbers (ie. PDOC00420) of the documents pasted below to 
find links to the others you may need. You will also find that the Expasy 
site  http://expasy.hcuge.ch  has links to many useful databases. You can 
find some other resource links from my labs web site too. Good Luck

FROM PROSITE: *******************************************


PROSITE: PDOC00420 (documentation)
************************************
* ATP synthase a subunit signature *
************************************

ATP synthase (proton-translocating ATPase) (EC 3.6.1.34) [1,2]  is a
component of the cytoplasmic membrane of eubacteria, the inner membrane of
mitochondria, and the thylakoid membrane of chloroplasts.  The ATPase 
complex is composed of an oligomeric  transmembrane  sector, called CF(0),  
which acts  as  a proton channel, and a catalytic core, termed coupling 
factor CF(1).

The CF(0) a subunit, also called protein 6,  is  a key component of the
proton channel; it  may  play  a  direct  role  in  translocating  protons
across the membrane. It  is  a  highly  hydrophobic  protein  that  has 
been predicted to contain 8 transmembrane regions [3].

Sequence comparison of a subunits from all available sources reveals 
very few conserved regions.  The  best conserved region is located in what 
is predicted to be the fifth transmembrane domain. This region contains 
three perfectly conserved residues:  an  arginine,  a  leucine  and an 
asparagine.Mutagenesis experiments carried  out  in Escherichia coli [4] 
have shown that the arginine is necessary  for  proton  translocation  and  
that its replacement by another amino acid  results  in  loss of ATPase 
activity. We selected this region as a signature pattern.

-Consensus pattern: [STAGN]-x-[STAG]-[LIVMF]-R-L-x-[SAGV]-N-[LIVMT]
                    [R is important for proton translocation]
-Sequences known to belong to this class detected by the pattern: ALL, 
except for the Mytilus edulis and Trypanosoma brucei subunits.
-Other sequence(s) detected in SWISS-PROT: 6.
-Last update: November 1997 / Pattern and text revised.

[ 1] Futai M., Noumi T., Maeda M.
     Annu. Rev. Biochem. 58:111-136(1989).
[ 2] Senior A.E.
     Physiol. Rev. 68:177-231(1988).
[ 3] Lewis M.L., Chang J.A., Simoni R.D.
     J. Biol. Chem. 265:10541-10550(1990).
[ 4] Cain B.D., Simoni R.D.
     J. Biol. Chem. 264:3292-3300(1989).
{END}


PROSITE: PDOC00137 (documentation)
**************************************************
* ATP synthase alpha and beta subunits signature *
**************************************************

ATP synthase (proton-translocating ATPase) (EC 3.6.1.34) [1,2]  is a
component of the cytoplasmic membrane of eubacteria, the inner membrane of
mitochondria, and the thylakoid membrane of chloroplasts.  The ATPase 
complex is composed of an oligomeric transmembrane sector, called CF(0), 
and a catalytic core, called coupling factor  CF(1).  The  former  acts  as 
a proton channel; the latter is composed of  five  subunits,  alpha,  beta,  
gamma,  delta  and  epsilon.  The sequences of   subunits  alpha  and  beta  
are  related  and  both contain  a nucleotide-binding site  for  ATP  and  
ADP.  The  beta  chain  has catalytic activity, while the alpha chain is a 
regulatory subunit.

Vacuolar ATPases [3] (V-ATPases)  are  responsible for acidifying a
variety of intracellular  compartments  in  eukaryotic cells.  Like  F-
ATPases,  they are oligomeric complexes  of  a transmembrane and a 
catalytic sector. The sequence of the  largest  subunit of the catalytic 
sector (70 Kd) is related to that of F-ATPase beta subunit, while a 60 Kd 
subunit, from the same sector, is related to the F-ATPases alpha subunit 
[4].

Archaebacterial membrane-associated  ATPases  are  composed of three
subunits.The alpha  chain  is  related  to  F-ATPases  beta chain and the 
beta chain is related to F-ATPases alpha chain [4].

A protein  highly  similar  to  F-ATPase  beta  subunits  is found [5]
in some bacterial apparatus  involved  in  a  specialized  protein export
pathway that proceeds without  signal  peptide  cleavage.  This protein is 
known as fliI in Bacillus and    Salmonella,    Spa47  (mxiB)  in  Shigella  
flexneri, HrpB6 in Xanthomonas campestris and yscN in Yersinia virulence 
plasmids.

In order to  detect these ATPase subunits, we took a segment of ten
amino-acid residues, containing two conserved serines, as a signature 
pattern.  The first serine seems  to  be  important  for  catalysis - in 
the ATPase alpha chain at least - as its mutagenesis causes catalytic 
impairment.

-Consensus pattern: P-[SAP]-[LIV]-[DNH]-x(3)-S-x-S
                    [The first S is a putative active site residue]
-Sequences known to belong to this class detected by the pattern: ALL, 
 except for the  archaebacterium  Sulfolobus  acidocaldarius ATPase alpha  
 chain where
 the first Ser is replaced by Gly.
-Other sequence(s) detected in SWISS-PROT: 33.

-Note: F-ATPase  alpha  and  beta  subunits,  V-ATPase  70  Kd subunit
and the archaebacterial ATPase alpha  subunit also  contain a copy of the
ATP-binding motifs A and B (see ).

-Last update: November 1997 / Pattern and text revised.

[ 1] Futai M., Noumi T., Maeda M.
     Annu. Rev. Biochem. 58:111-136(1989).
[ 2] Senior A.E.
     Physiol. Rev. 68:177-231(1988).
[ 3] Nelson N.
     J. Bioenerg. Biomembr. 21:553-571(1989).
[ 4] Gogarten J.P., Kibak H., Dittrich P., Taiz L., Bowman E.J., Bowman
B.J., Manolson M.F., Poole R.J., Date T., Oshima T., Konishi J., Denda
K., Yoshida M. Proc. Natl. Acad. Sci. U.S.A. 86:6661-665(1989).
[ 5] Dreyfus G., Williams A.W., Kawagishi I., MacNab R.M.
     J. Bacteriol. 175:3131-3138(1993).
{END}

Kenneth P. Mitton, Ph.D.
Ophthalmology Department
Kellogg Eye Center / rm 540
University of Michigan
Ann Arbor, MI 48105
313-936-8370
313-647-0228
kpmitton@umich.edu


http://141.214.184.151/mitton.html