Structure-first census of JAMM catalytic-site modification across the MPN fold: pipeline, measurement tables and raw structural searches

Abstract

Pipeline and data for a structure-first census of the JAMM zinc isopeptidase site across 3,884 verified MPN-fold proteins. Catalytic-site positions are read by three-dimensional superposition onto a reference MPN+ domain (PDB 1R5X chain A) rather than by sequence alignment; fold membership is verified by secondary-structure topology against characterized anchors and unrelated-fold negative controls; and every loss call is required to rest on a confidently modelled region of the predicted structure. The archive contains the complete pipeline (steps 01–14), the measurement and supplementary tables including the verified census, the structure-derived alignment and phylogeny, the four manuscript figures, and the raw output of all 69 Foldseek webserver searches. The raw search output is included because it is the only part of the analysis that cannot be regenerated: the webserver searches live databases and caps each query at 1,000 accepted hits, so the same query returns a different result set later. AlphaFold models and PDB structures are not included; they are regenerable from the accession lists in the census table. Step 14 regenerates the published census from the deposited tables and asserts its member and class counts, so the archive can be verified without re-running any search.