TAILIEUCHUNG - Báo cáo khóa học: The PAS fold A redefinition of the PAS domain based upon structural prediction

In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current pro-tein sequence databases are predicted to contain a PAS domainbaseduponaminoacid sequence theproblemswith the current annotationof thePASdomain is that this domain exhibits limited similarity at the amino acid sequence level. It is therefore essential, when using proteins with low-sequence similarities, to apply profile hidden Markov model searches for the PASdomain-con-tainingproteins, as for thePFAMdatabase | Eur. J. Biochem. 271 1198-1208 2004 FEBS 2004 doi The PAS fold A redefinition of the PAS domain based upon structural prediction Marco H. Hefti1 I Kees-Jan Francoijs1 Sacco C. de Vries1 Ray Dixon2 and Jacques Vervoort1 1 Laboratory of Biochemistry Wageningen University the Netherlands 2Department of Molecular Microbiology John Innes Centre Norwich UK In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current protein sequence databases are predicted to contain a PAS domain based upon amino acid sequence alignments. One of the problems with the current annotation of the PAS domain is that this domain exhibits limited similarity at the amino acid sequence level. It is therefore essential when using proteins with low-sequence similarities to apply profile hidden Markov model searches for the PAS domain-containing proteins as for the PFAM database. From recent 3D X-ray and NMR structures however PAS domains appear to have a conserved 3D fold as shown here by structural alignment of the six representative 3D-structures from the PDB database. Large-scale modelling of the PAS sequences from the PFAM database against the 3D-structures of these six structural prototypes was performed. All 3D models generated 5700 were evaluated using PROSAII. We conclude from our large-scale modelling studies that the PAS and PAC motifs which are separately defined in the PFAM database are directly linked and that these two motifs form the PAS obld. The xxitiíng subiivisinn m PAS and PCC motifs as used by the PFAM and SMART databases appears to be caused by ma or differences in sequences in the region connecting these two motifs. This region as has been shown by Gardner and coworkers for human PAS kinaee Amezcua . Harper . Rutter J. Gardner . 2002 Structure 10 1349-1361 1 is very flexible and adopts different conformations .

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