circular permutation of proteins in nature

[Andrei Lupas]

Two articles appeared in TIBS this year with examples for circular 
permutations in the sequence of natural proteins. I contributed a
third example to the newsgroup bionet.journals.letters.tibs that I
append to this message. Following a suggestion by Robert Russel who
authored the first of the two TIBS articles, I am posting this message
to the larger bionet groups in the hope that others will have examples
to add to our list which so far contains:

- plant swaposins (containing a permutated saposin domain)
- Fibrobacter succinogenes beta-glucanase
- Clostridium thermocellum OlpB (containing a permutated SLH domain).

Sincerely,
Andrei Lupas

--------------------------------------------------------------------------

   Two recent contributions to TIBS (Ponting and Russel, May issue [1]; and 
Heinemann and Hahn, September issue [2]) have described examples of circular 
permutation in the sequence of natural proteins. I would like to add a 
third example, which I described in J. Bacteriol. last year: the SLH domain of
cell wall-attached proteins in eubacteria [3].
   The SLH domain (for Surface Layer Homology) is a repetitive, modular 
element that occurs in one, two, or three copies at the N- or C-terminal end 
of many cell-wall associated bacterial proteins. Recently, the group of Pierre
Beguin has shown that it mediates attachment to the cell wall as well as 
interactions with other SLH domains [4]. The predicted secondary structure of 
the module is that of two helices flanking a short beta strand. The borders of
the module are clearly defined by the N- or C-termini of the proteins, or by 
the start of other structural domains, such as the coiled-coil rod in 
Thermotoga maritima Omp alpha [5]. In most proteins, the SLH domains start 
with a conserved sequence preceeding helix 1 and end after helix 2. In three 
proteins from Clostridium thermocellum, which may be structural proteins of 
the cellulosome [6], the first SLH domain is missing helix 1, which is 
appended to the C-terminus of the third SLH domain, clearly indicating a 
circular permutation event in the evolution of these proteins. 


                    Helix 1                         Helix 2
PHD              HHHHHHHHHHHHH  SSS              HHHHHHHHHHHHH  

cons     .F.DV.....WA..........GI..G.PDG.F.....ITR.E.A....R.L..............

Omp     ^FFPDVPK-DHWAYEYVWKLWQRGIFIGYPDGEFKGDRYITRYEAATAVSRLLDFIEQKMLAGAS

SLP  ^attPFTDVKD-DAPYASAVARLYALNITNGVGDPKFGVDQPVTRAQMITFVNRMLGYEDLAEMAKSEKS
         AFKDVPQ-NHWAVGQINLAYKLGLAQGVGNGKFDPNSELRYAQALAFVLRALGFKDLD

XynX     TFNDIK--DNWAKDVIEVLASRHIVEGMTDTQYEPSKTVTRAEFTAMILKLLNIKEEAYNG
         EFSDVKN-GDWYANAIEAAYKAGIIEGDGKN-MRPNDSITREEMTSIAMRAYEMLTSYKEENIGAT
         SFNDDKSISDWAKNVVANAAKLGIINGEPSNVFAPKGIATRAEAAAIIYGLLEKSNNL*

OlpB     apteieeptpsdvpgaiggehr
                               AYLRGYPDGSFRPERNITRAEAAVIFAKLLGADESYGAQSAS
         PYSDLAD-THWAAWAIKFATSQGLFKGYPDGTFKPDQNITRAEFATVVLHFLTKVKGQEIMSKL[8]
         KFDDCV--GHWAQEFIEKLTSLGYISGYPDGTFKPQNYIKRSESVALINRALERGPLNGAPK
         LFPDVNE-SYWAFGDIMDGALD
                               hsyiiedekekfvklled*

Legend:
PHD     Secondary structure prediction by the method of Rost and Sander
cons    residues conserved in a majority of known SLH domains
Omp     Thermotoga maritima outer membrane protein alpha
SLP     Acetogenium kivui surface layer protein
XynX    Clostridium thermocellum xylanase
OlpB    Clostridium thermocellum structural protein of the cellulosome (?)
^       protein N-terminus
*       protein C-terminus

[1] Ponting, C. P. and Russel, R. B. (1995) Trends Biochem. Sci. 20, 179-180
[2] Heinemann, U. and Hahn, M. (1995) Trends Biochem. Sci. 20, 349-350
[3] Lupas, A. et al. (1994) J. Bacteriol. 176, 1224-1233
[4] Lemaire, M. et al. (1995) J. Bacteriol. 177, 2451-2459
[5] Lupas, A. et al. (1995) J. Mol. Biol. 248, 180-189
[6] Fujino, T. et al. (1993) J. Bacteriol. 175, 1891-1899

----------------------------------------------------------------------------
Andrei Lupas, PhD                                   lupas at vms.biochem.mpg.de
Abteilung Strukturbiologie
Max-Planck-Institut fuer Biochemie
D-82152 Martinsried, Germany