Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation
HutZ is the sole heme storage protein identified in the pathogenic bacterium Vibrio cholerae and is required for optimal heme utilization. However, no heme oxygenase activity has been observed with this protein. Thus far, HutZ’s structure and heme-binding mechanism are unknown.
We report the first crystal structure of HutZ in a homodimer determined at 2.0 Å resolution. The HutZ structure adopted a typical split-barrel fold. Through a docking study and site-directed mutagenesis, a heme-binding model for the HutZ dimer is proposed. Very interestingly, structural superimposition of HutZ and its homologous protein HugZ, a heme oxygenase from Helicobacter pylori, exhibited a structural mismatch of one amino acid residue in β6 of HutZ, although residues involved in this region are highly conserved in both proteins. Derived homologous models of different single point variants with model evaluations suggested that Pro140 of HutZ, corresponding to Phe215 of HugZ, might have been the main contributor to the structural mismatch. This mismatch initiates more divergent structural characteristics towards their C-terminal regions, which are essential features for the heme-binding of HugZ as a heme oxygenase.
HutZ’s deficiency in heme oxygenase activity might derive from its residue shift relative to the heme oxygenase HugZ. This residue shift also emphasized a limitation of the traditional template selection criterion for homology modeling.
- Wyckoff EE, Mey AR, Payne SM: Iron acquisition in vibrio cholerae. Biometals 2007,20(3–4):405–416. CrossRef
- Griffiths GL, Sigel SP, Payne SM, Neilands JB: vibriobactin, a siderophore from vibrio cholerae. J Biol Chem 1984,259(1):383–385.
- Seliger SS, Mey AR, Valle AM, Payne SM: The two TonB systems of vibrio cholerae: redundant and specific functions. Mol Microbiol 2001,39(3):801–812. CrossRef
- Mey AR, Wyckoff EE, Oglesby AG, Rab E, Taylor RK, Payne SM: Identification of the vibrio cholerae enterobactin receptors VctA and IrgA: IrgA is not required for virulence. Infect Immun 2002,70(7):3419–3426. CrossRef
- Wyckoff EE, Valle AM, Smith SL, Payne SM: A multifunctional ATP-binding cassette transporter system from vibrio cholerae transports vibriobactin and enterobactin. J Bacteriol 1999,181(24):7588–7596.
- Rogers MB, Sexton JA, DeCastro GJ, Calderwood SB: Identification of an operon required for ferrichrome iron utilization in vibrio cholerae. J Bacteriol 2000,182(8):2350–2353. CrossRef
- Stoebner JA, Payne SM: Iron-regulated hemolysin production and utilization of heme and hemoglobin by vibrio cholerae. Infect Immun 1988,56(11):2891–2895.
- Henderson DP, Payne SM: Cloning and characterization of the vibrio cholerae genes encoding the utilization of iron from haemin and haemoglobin. Mol Microbiol 1993,7(3):461–469. CrossRef
- Occhino DA, Wyckoff EE, Henderson DP, Wrona TJ, Payne SM: vibrio cholerae iron transport: haem transport genes are linked to one of two sets of tonB, exbB, exbD genes. Mol Microbiol 1998,29(6):1493–1507. CrossRef
- Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al.: Database resources of the national center for biotechnology information. Nucleic Acids Res 2008,36(Database issue):D13-D21.
- Wyckoff EE, Schmitt M, Wilks A, Payne SM: HutZ is required for efficient heme utilization in vibrio cholerae. J Bacteriol 2004,186(13):4142–4151. CrossRef
- Guo Y, Guo G, Mao X, Zhang W, Xiao J, Tong W, Liu T, Xiao B, Liu X, Feng Y, et al.: Functional identification of HugZ, a heme oxygenase from helicobacter pylori. BMC Microbiol 2008, 8:226. CrossRef
- Hu Y, Jiang F, Guo Y, Shen X, Zhang Y, Zhang R, Guo G, Mao X, Zou Q, Wang DC: Crystal structure of HugZ, a novel heme oxygenase from helicobacter pylori. J Biol Chem 2011,286(2):1537–1544. CrossRef
- Zhang R, Zhang J, Guo G, Mao X, Tong W, Zhang Y, Wang DC, Hu Y, Zou Q: Crystal structure of Campylobacter jejuni ChuZ: a split-barrel family heme oxygenase with a novel heme-binding mode. Biochem Biophys Res Commun 2011,415(1):82–87. CrossRef
- Hirotsu S, Chu GC, Unno M, Lee DS, Yoshida T, Park SY, Shiro Y, Ikeda-Saito M: The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of corynebacterium diphtheriae. J Biol Chem 2004,279(12):11937–11947. CrossRef
- Zhu W, Wilks A, Stojiljkovic I: Degradation of heme in gram-negative bacteria: the product of the hemO gene of Neisseriae is a heme oxygenase. J Bacteriol 2000,182(23):6783–6790. CrossRef
- Skaar EP, Gaspar AH, Schneewind O: Bacillus anthracis IsdG, a heme-degrading monooxygenase. J Bacteriol 2006,188(3):1071–1080. CrossRef
- Suits MD, Pal GP, Nakatsu K, Matte A, Cygler M, Jia Z: Identification of an Escherichia coli O157:H7 heme oxygenase with tandem functional repeats. Proc Natl Acad Sci U S A 2005,102(47):16955–16960. CrossRef
- Anfinsen CB: Principles that govern the folding of protein chains. Science 1973,181(96):223–230. CrossRef
- Wilks A: The ShuS protein of Shigella dysenteriae is a heme-sequestering protein that also binds DNA. Arch Biochem Biophys 2001,387(1):137–142. CrossRef
- Otwinowski Z, Minor W: Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 1997, 276:307–326. CrossRef
- Emsley P, Cowtan K: Coot: model-building tools for molecular graphics. Acta Crystallogr D: Biol Crystallogr 2004,60(Pt 12 Pt 1):2126–2132. CrossRef
- Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC: PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D: Biol Crystallogr 2002,58(Pt 11):1948–1954. CrossRef
- Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 2009,30(16):2785–2791. CrossRef
- Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A: Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics 2006, Chapter 5:Unit 5 6.
- Wallner B, Elofsson A: Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 2006,15(4):900–913. CrossRef
- Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
BMC Structural Biology
- Online Date
- September 2012
- Online ISSN
- BioMed Central
- Additional Links
- Crystal structure
- Homology modeling
- Author Affiliations
- 1. State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
- 3. College of Life Sciences, Hebei University, Baoding, 071002, China
- 2. Cancer Research Center, School of Medicine, Shandong University, Jinan, 250012, China