Database accession: MF7000284
Name: Putative NTP pyrophosphohydrolase
PDB ID: 3nl9
Experimental method: X-ray (1.78 Å)
Assembly: Homodimer
Source organism: Exiguobacterium sibiricum
Primary publication of the structure:
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
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.
(2010) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66: 1237-44
PMID: 20944217
Abstract:
The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-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 α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: HAD family hydrolase
Source organism: Exiguobacterium sibiricum
Length: 170 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLKETYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLEAEVVRQMKEKA
UniProtKB AC: B1YMF4 (positions: 2-170)
Coverage: 99%
Name: HAD family hydrolase
Source organism: Exiguobacterium sibiricum
Length: 170 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLKETYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLEAEVVRQMKEKA
UniProtKB AC: B1YMF4 (positions: 2-170)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Phosphoribosyl-ATP pyrophosphohydrolase
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
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′ and 3′ 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 A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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