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Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

Bottom Line: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold.The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins.Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India.

ABSTRACT

Background: Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification.

Results: On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc.

Conclusions: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

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SCOP folds only in new classification28 folds present only in newly classified complexes. The fold exhibited by maximum number of newly classified complexes are those which are involved in DNA damage repair functions like Lesion bypass DNA Polymerase, MutS domain, Glycosylase. Numbers represent the respective names of SCOP fold in the Figure 1. ATP-dependent DNA ligase DNA-binding domain, 2. Cryptochrome/photolyase FAD-binding domain, 3. DNA-clamp, 4. Double-stranded β-helix, 5. GCM domain, 6. Hcp1-like, 7. Metallo-dependent phosphatases, 8. Phage replication organizer domain, 9. SPOC domain-like, vWA-like, 10. Thioredoxin fold, 11. Type II DNA topoisomerase ,12. DNA-binding domain of intron-encoded endonucleases, 13. Phospholipase D/nuclease, 14. Replication modulator SeqA, C-terminal DNA-binding domain, 15. SMAD MH1 domain, 16. UDP-Glycosyltransferase/glycogen phosphorylase, 17. N-terminal domain of MutM-like DNA repair proteins, 18. P-loop containing nucleoside triphosphate hydrolases, 19. SAM domain-like, 20. SRF-like, 21. Zinc finger design, 22. Origin of replication-binding domain, RBD-like, 23. Ribonuclease H-like motif, 24. PUA domain-like, 25. DNA-glycosylase, 26. Putative DNA-binding domain, 27. DNA-repair protein MutS, domain III, 28. Lesion bypass DNA polymerase (Y-family)
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Figure 9: SCOP folds only in new classification28 folds present only in newly classified complexes. The fold exhibited by maximum number of newly classified complexes are those which are involved in DNA damage repair functions like Lesion bypass DNA Polymerase, MutS domain, Glycosylase. Numbers represent the respective names of SCOP fold in the Figure 1. ATP-dependent DNA ligase DNA-binding domain, 2. Cryptochrome/photolyase FAD-binding domain, 3. DNA-clamp, 4. Double-stranded β-helix, 5. GCM domain, 6. Hcp1-like, 7. Metallo-dependent phosphatases, 8. Phage replication organizer domain, 9. SPOC domain-like, vWA-like, 10. Thioredoxin fold, 11. Type II DNA topoisomerase ,12. DNA-binding domain of intron-encoded endonucleases, 13. Phospholipase D/nuclease, 14. Replication modulator SeqA, C-terminal DNA-binding domain, 15. SMAD MH1 domain, 16. UDP-Glycosyltransferase/glycogen phosphorylase, 17. N-terminal domain of MutM-like DNA repair proteins, 18. P-loop containing nucleoside triphosphate hydrolases, 19. SAM domain-like, 20. SRF-like, 21. Zinc finger design, 22. Origin of replication-binding domain, RBD-like, 23. Ribonuclease H-like motif, 24. PUA domain-like, 25. DNA-glycosylase, 26. Putative DNA-binding domain, 27. DNA-repair protein MutS, domain III, 28. Lesion bypass DNA polymerase (Y-family)

Mentions: Also, there were 28 folds which were present only in new complexes, suggesting emergence of structures of complexes performing new functions (Figure 9). The proteins possessing DNA-repair function is present exclusively in the newly classified complexes like Y-family DNA polymerases which are known to bypass a lesion in DNA, DNA glycosylases and MutS DNA-repair proteins.


Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

SCOP folds only in new classification28 folds present only in newly classified complexes. The fold exhibited by maximum number of newly classified complexes are those which are involved in DNA damage repair functions like Lesion bypass DNA Polymerase, MutS domain, Glycosylase. Numbers represent the respective names of SCOP fold in the Figure 1. ATP-dependent DNA ligase DNA-binding domain, 2. Cryptochrome/photolyase FAD-binding domain, 3. DNA-clamp, 4. Double-stranded β-helix, 5. GCM domain, 6. Hcp1-like, 7. Metallo-dependent phosphatases, 8. Phage replication organizer domain, 9. SPOC domain-like, vWA-like, 10. Thioredoxin fold, 11. Type II DNA topoisomerase ,12. DNA-binding domain of intron-encoded endonucleases, 13. Phospholipase D/nuclease, 14. Replication modulator SeqA, C-terminal DNA-binding domain, 15. SMAD MH1 domain, 16. UDP-Glycosyltransferase/glycogen phosphorylase, 17. N-terminal domain of MutM-like DNA repair proteins, 18. P-loop containing nucleoside triphosphate hydrolases, 19. SAM domain-like, 20. SRF-like, 21. Zinc finger design, 22. Origin of replication-binding domain, RBD-like, 23. Ribonuclease H-like motif, 24. PUA domain-like, 25. DNA-glycosylase, 26. Putative DNA-binding domain, 27. DNA-repair protein MutS, domain III, 28. Lesion bypass DNA polymerase (Y-family)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472317&req=5

Figure 9: SCOP folds only in new classification28 folds present only in newly classified complexes. The fold exhibited by maximum number of newly classified complexes are those which are involved in DNA damage repair functions like Lesion bypass DNA Polymerase, MutS domain, Glycosylase. Numbers represent the respective names of SCOP fold in the Figure 1. ATP-dependent DNA ligase DNA-binding domain, 2. Cryptochrome/photolyase FAD-binding domain, 3. DNA-clamp, 4. Double-stranded β-helix, 5. GCM domain, 6. Hcp1-like, 7. Metallo-dependent phosphatases, 8. Phage replication organizer domain, 9. SPOC domain-like, vWA-like, 10. Thioredoxin fold, 11. Type II DNA topoisomerase ,12. DNA-binding domain of intron-encoded endonucleases, 13. Phospholipase D/nuclease, 14. Replication modulator SeqA, C-terminal DNA-binding domain, 15. SMAD MH1 domain, 16. UDP-Glycosyltransferase/glycogen phosphorylase, 17. N-terminal domain of MutM-like DNA repair proteins, 18. P-loop containing nucleoside triphosphate hydrolases, 19. SAM domain-like, 20. SRF-like, 21. Zinc finger design, 22. Origin of replication-binding domain, RBD-like, 23. Ribonuclease H-like motif, 24. PUA domain-like, 25. DNA-glycosylase, 26. Putative DNA-binding domain, 27. DNA-repair protein MutS, domain III, 28. Lesion bypass DNA polymerase (Y-family)
Mentions: Also, there were 28 folds which were present only in new complexes, suggesting emergence of structures of complexes performing new functions (Figure 9). The proteins possessing DNA-repair function is present exclusively in the newly classified complexes like Y-family DNA polymerases which are known to bypass a lesion in DNA, DNA glycosylases and MutS DNA-repair proteins.

Bottom Line: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold.The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins.Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India.

ABSTRACT

Background: Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification.

Results: On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc.

Conclusions: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

Show MeSH
Related in: MedlinePlus