9isp | pdb_00009isp
DUF2436 domain which is frequently found in virulence proteins from Porphyromonas gingivalis
Structural highlights
FunctionPRTH_PORGI Cleaves human complement component C3. May enable P.gingivalis to evade complement-mediated killing during the immune response. Plays an important role in soft tissue infections and is a virulence factor. Publication Abstract from PubMedPorphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 A resolution, revealing a noncanonical beta-jelly-roll sandwich topology with two antiparallel beta-sheets and one short alpha-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of beta1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9-5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed. First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis.,Kim B, Hwang J, Im S, Do H, Shim YS, Lee JH Acta Crystallogr F Struct Biol Commun. 2024 Oct 1;80(Pt 10):252-262. doi: , 10.1107/S2053230X24008185. Epub 2024 Sep 26. PMID:39325582[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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