Crystal structure of HP0721, a novel secreted protein from <i>Helicobacter pylori</i>

Cioci, Gianluca; Terradot, Laurent; Dian, Cyril; Mueller-Dieckmann, Christoph; Leonard, Gordon A.

doi:10.1002/prot.22988

Cited by 6 publications

(2 citation statements)

References 23 publications

(21 reference statements)

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“…A survey of structures determined in the Protein Structure Initiative indicates that 5% of structures of proteins of unknown function have unknown ligands bound 24 . For example, a similar electron density feature was observed in another structure of a helical protein with unknown function 25 . In the structure of HP0721 from Helicobacter pylori (PDB 2XRH), the unknown ligand was modeled as nicotinic acid based on the strong interaction with an arginine sidechain, implying a carboxylate functional group.…”

Section: Discussionsupporting

confidence: 57%

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

McKay,

Cheng,

Tanner

2023

Sci Rep

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The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C2221 and P3221) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11–57 and 102–148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

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Section: Discussionsupporting

confidence: 57%

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

McKay,

Cheng,

Tanner

2023

Sci Rep

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“…,Ambrosio et al (2005),Araç et al (2012),Bian et al (2010),Bond et al (2001),Brown et al (2002),Chattopadhyay et al (2008),Chen et al (2007),Cianci et al (2001),Cioci et al (2011),Dauter et al (1999),Debreczeni, Bunkó czi et al (2003),,Devesse et al (2011),Doan & Dokland (2003), Enroth & Ake (2008), Fabian et al (2013), Fukakusa et al (2012), Gordon et al (2001), Goulet et al (2010), Guimarã es et al (2009), Ivanov et al (2010), Klock et al (2005), Lartigue et al (2004), Li et al (2002), Li et al (2008), Li et al (2014), Liu, Gui et al (2014), Liu et al (2000), Machius et al (2007), Micossi et al (2002), Moynie et al (2013), Mueller et al (2011), Mueller-Dieckmann et al (2007), Mü ller et al (2011), Ni, Benning et al (2008), Ni, Sheldrick et al (2008), Okada et al (2008), Olsen et al (2004), Pal et al (2008), Phillips et al (2004), Pieren et al (2006), Popovic et al (2012), Rajasekaran et al (2013), Rodamilans et al (2007), Ru et al (2012), Rudiñ o-Piñ era et al (2007), Sarma & Karplus (2006), Sarma et al (2010, 2012), Shinobu et al (2010), Stegmann et al (2009), Thomas et al (2009), Thorsell et al (2009), Trempe et al (2005), Vasur et al (2006), Watanabe et al (2005), Weiss et al (2004), Yogavel et al (2014), Zebisch et al (2013) and Zhu et al (2012).…”

mentioning

confidence: 99%

Against the odds?De novostructure determination of a pilin with two cysteine residues by sulfur SAD

Gorgel

Bøggild

Ulstrup

et al. 2015

Acta Cryst D Biol Crystallogr

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Exploiting the anomalous signal of the intrinsic S atoms to phase a protein structure is advantageous, as ideally only a single well diffracting native crystal is required. However, sulfur is a weak anomalous scatterer at the typical wavelengths used for X-ray diffraction experiments, and therefore sulfur SAD data sets need to be recorded with a high multiplicity. In this study, the structure of a small pilin protein was determined by sulfur SAD despite several obstacles such as a low anomalous signal (a theoretical Bijvoet ratio of 0.9% at a wavelength of 1.8 Å), radiation damage-induced reduction of the cysteines and a multiplicity of only 5.5. The anomalous signal was improved by merging three data sets from different volumes of a single crystal, yielding a multiplicity of 17.5, and a sodium ion was added to the substructure of anomalous scatterers. In general, all data sets were balanced around the threshold values for a successful phasing strategy. In addition, a collection of statistics on structures from the PDB that were solved by sulfur SAD are presented and compared with the data. Looking at the quality indicator R(anom)/R(p.i.m.), an inconsistency in the documentation of the anomalous R factor is noted and reported.

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Crystal structures of the isochorismatase domains from Vibrio anguillarum

Deng

2017

Biochemical and Biophysical Research Communications

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Crystal structure of HP0721, a novel secreted protein from Helicobacter pylori

Cited by 6 publications

References 23 publications

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

Against the odds?De novostructure determination of a pilin with two cysteine residues by sulfur SAD

Crystal structures of the isochorismatase domains from Vibrio anguillarum

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