{"entry": {"accession": "MF7000284", "general": {"name": "Putative NTP pyrophosphohydrolase", "pdb_id": "3nl9", "exp_method": "X-ray", "resolution": "1.78", "assembly": "Homodimer", "source_organism": "Exiguobacterium sibiricum", "publication": {"pmid": "20944217", "authors": "Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA", "title": "Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.", "journal": "Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.", "year": "2010", "issue": "Pt 10", "volume": "66", "pages": "1237-44", "abstract": "The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78\u2005\u00c5 resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-\u03b1-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other \u03b1-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity."}}, "function": null, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "HAD family hydrolase", "source_organism": "Exiguobacterium sibiricum", "uniprot": {"id": "B1YMF4", "start": "2", "end": "170", "coverage": "99%", "sequence": "MKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLKETYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLEAEVVRQMKEKA", "length": "170"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "6", "region_end": "18"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "30", "region_end": "46"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "46", "region_end": "53"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "56", "region_end": "80"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "86", "region_end": "113"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "116", "region_end": "129"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "155", "region_end": "171"}, {"region_type": "pfam", "region_id": "PF01503", "region_name": "Phosphoribosyl-ATP pyrophosphohydrolase", "region_start": "10", "region_end": "126"}]}}, {"id": "A-2", "name": "HAD family hydrolase", "source_organism": "Exiguobacterium sibiricum", "uniprot": {"id": "B1YMF4", "start": "2", "end": "170", "coverage": "99%", "sequence": "MKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLKETYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLEAEVVRQMKEKA", "length": "170"}, "regions": {"region": {"region_type": "pfam", "region_id": "PF01503", "region_name": "Phosphoribosyl-ATP pyrophosphohydrolase", "region_start": "10", "region_end": "126"}}}]}, "evidence": {"evidence_level": "Direct evidence", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "Phosphoribosyl-ATP pyrophosphohydrolase", "complex_evidence": "Phosphoribosyl-ATP pyrophosphohydrolases show a very unusual interlaced segment-swapped dimer, which implies that this obligatory dimer assembly is important for their function. Size-exclusion chromatography combined with static light scattering confirmed that the dimer is the major oligomeric state in solution (PMID:20944217). Upon dimer formation, DR2231 helices 2 and 3 from one monomer stack antiparallel to helices 2\u2032 and 3\u2032 of the other monomer, respectively. A stable four-helix bundle is formed in the center. The intertwining of the two hairpin structures produces an extensive subunit-subunit interface (PMID:21733847).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "A-2", "support": "N/A"}]}, "related_structures": {"id": ["MF7000284", "MF7000232", "MF7000233"]}}}