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EMBO J. Dec 15, 1995; 14(24): 6067–6077.
PMCID: PMC394731

Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.

Abstract

The molecular structure of the flavohemoglobin from Alcaligenes eutrophus has been determined to a resolution of 1.75 A and refined to an R-factor of 19.6%. The protein comprises two fused modules: a heme binding module, which belongs to the globin family, and an FAD binding oxidoreductase module, which adopts a fold like ferredoxin reductase. The most striking deviation of the bacterial globin structure from those of other species is the movement of helix E in a way to provide more space in the vicinity of the distal heme binding site. A comparison with other members of the ferredoxin reductase family shows similar tertiary structures for the individual FAD and NAD binding domains but largely different interdomain orientations. The heme and FAD molecules approach each other to a minimal distance of 6.3 A and adopt an interplanar angle of 80 degrees. The electron transfer from FAD to heme occurs in a predominantly polar environment and may occur directly or be mediated by a water molecule.

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  • Andrews SC, Shipley D, Keen JN, Findlay JB, Harrison PM, Guest JR. The haemoglobin-like protein (HMP) of Escherichia coli has ferrisiderophore reductase activity and its C-terminal domain shares homology with ferredoxin NADP+ reductases. FEBS Lett. 1992 May 18;302(3):247–252. [PubMed]
  • Arents G, Love WE. Glycera dibranchiata hemoglobin. Structure and refinement at 1.5 A resolution. J Mol Biol. 1989 Nov 5;210(1):149–161. [PubMed]
  • Aronson HE, Royer WE, Jr, Hendrickson WA. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Sci. 1994 Oct;3(10):1706–1711. [PMC free article] [PubMed]
  • Bashford D, Chothia C, Lesk AM. Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol. 1987 Jul 5;196(1):199–216. [PubMed]
  • Bolognesi M, Onesti S, Gatti G, Coda A, Ascenzi P, Brunori M. Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution. J Mol Biol. 1989 Feb 5;205(3):529–544. [PubMed]
  • Brünger AT, Kuriyan J, Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. [PubMed]
  • Bruns CM, Karplus PA. Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states. J Mol Biol. 1995 Mar 17;247(1):125–145. [PubMed]
  • Chen ZW, Koh M, Van Driessche G, Van Beeumen JJ, Bartsch RG, Meyer TE, Cusanovich MA, Mathews FS. The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science. 1994 Oct 21;266(5184):430–432. [PubMed]
  • Correll CC, Batie CJ, Ballou DP, Ludwig ML. Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S]. Science. 1992 Dec 4;258(5088):1604–1610. [PubMed]
  • Correll CC, Ludwig ML, Bruns CM, Karplus PA. Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin. Protein Sci. 1993 Dec;2(12):2112–2133. [PMC free article] [PubMed]
  • Cramm R, Siddiqui RA, Friedrich B. Primary sequence and evidence for a physiological function of the flavohemoprotein of Alcaligenes eutrophus. J Biol Chem. 1994 Mar 11;269(10):7349–7354. [PubMed]
  • Ermler U, Siddiqui RA, Cramm R, Schröder D, Friedrich B. Crystallization and preliminary X-ray diffraction studies of a bacterial flavohemoglobin protein. Proteins. 1995 Apr;21(4):351–353. [PubMed]
  • Eschenbrenner M, Coves J, Fontecave M. Ferric reductases in Escherichia coli: the contribution of the haemoglobin-like protein. Biochem Biophys Res Commun. 1994 Jan 14;198(1):127–131. [PubMed]
  • Favey S, Labesse G, Vouille V, Boccara M. Flavohaemoglobin HmpX: a new pathogenicity determinant in Erwinia chrysanthemi strain 3937. Microbiology. 1995 Apr;141(Pt 4):863–871. [PubMed]
  • Fermi G, Perutz MF, Shaanan B, Fourme R. The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. J Mol Biol. 1984 May 15;175(2):159–174. [PubMed]
  • Goodin DB, McRee DE. The Asp-His-Fe triad of cytochrome c peroxidase controls the reduction potential, electronic structure, and coupling of the tryptophan free radical to the heme. Biochemistry. 1993 Apr 6;32(13):3313–3324. [PubMed]
  • Hol WG, van Duijnen PT, Berendsen HJ. The alpha-helix dipole and the properties of proteins. Nature. 1978 Jun 8;273(5662):443–446. [PubMed]
  • Iwaasa H, Takagi T, Shikama K. Amino acid sequence of yeast hemoglobin. A two-domain structure. J Mol Biol. 1992 Oct 5;227(3):948–954. [PubMed]
  • Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. [PubMed]
  • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. [PubMed]
  • Karplus PA, Daniels MJ, Herriott JR. Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family. Science. 1991 Jan 4;251(4989):60–66. [PubMed]
  • Lu G, Campbell WH, Schneider G, Lindqvist Y. Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases. Structure. 1994 Sep 15;2(9):809–821. [PubMed]
  • Drennan CL, Huang S, Drummond JT, Matthews RG, Lidwig ML. How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. Science. 1994 Dec 9;266(5191):1669–1674. [PubMed]
  • Mathews FS, Chen ZW, Bellamy HD, McIntire WS. Three-dimensional structure of p-cresol methylhydroxylase (flavocytochrome c) from Pseudomonas putida at 3.0-A resolution. Biochemistry. 1991 Jan 8;30(1):238–247. [PubMed]
  • May AC, Johnson MS. Protein structure comparisons using a combination of a genetic algorithm, dynamic programming and least-squares minimization. Protein Eng. 1994 Apr;7(4):475–485. [PubMed]
  • Moser CC, Keske JM, Warncke K, Farid RS, Dutton PL. Nature of biological electron transfer. Nature. 1992 Feb 27;355(6363):796–802. [PubMed]
  • Neidle EL, Hartnett C, Ornston LN, Bairoch A, Rekik M, Harayama S. Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases. J Bacteriol. 1991 Sep;173(17):5385–5395. [PMC free article] [PubMed]
  • Nishida H, Inaka K, Yamanaka M, Kaida S, Kobayashi K, Miki K. Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution. Biochemistry. 1995 Mar 7;34(9):2763–2767. [PubMed]
  • Phillips SE. Structure and refinement of oxymyoglobin at 1.6 A resolution. J Mol Biol. 1980 Oct 5;142(4):531–554. [PubMed]
  • Poole RK, Ioannidis N, Orii Y. Reactions of the Escherichia coli flavohaemoglobin (Hmp) with oxygen and reduced nicotinamide adenine dinucleotide: evidence for oxygen switching of flavin oxidoreduction and a mechanism for oxygen sensing. Proc Biol Sci. 1994 Mar 22;255(1344):251–258. [PubMed]
  • Probst I, Schlegel HG. Respiratory components and oxidase activities in Alcaligenes eutrophus. Biochim Biophys Acta. 1976 Aug 13;440(2):412–428. [PubMed]
  • Probst I, Wolf G, Schlegel HG. An oxygen-binding flavohemoprotein from Alcaligenes eutrophus. Biochim Biophys Acta. 1979 Feb 26;576(2):471–478. [PubMed]
  • Pittsyn OB. Invariant features of globin primary structure and coding of their secondary structure. J Mol Biol. 1974 Sep 15;88(2):287–300. [PubMed]
  • Ramachandran GN, Venkatachalam CM, Krimm S. Stereochemical criteria for polypeptide and protein chain conformations. 3. Helical and hydrogen-bonded polypeptide chains. Biophys J. 1966 Nov;6(6):849–872. [PMC free article] [PubMed]
  • Royer WE., Jr High-resolution crystallographic analysis of a co-operative dimeric hemoglobin. J Mol Biol. 1994 Jan 14;235(2):657–681. [PubMed]
  • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. [PubMed]
  • Steigemann W, Weber E. Structure of erythrocruorin in different ligand states refined at 1.4 A resolution. J Mol Biol. 1979 Jan 25;127(3):309–338. [PubMed]
  • Vasudevan SG, Armarego WL, Shaw DC, Lilley PE, Dixon NE, Poole RK. Isolation and nucleotide sequence of the hmp gene that encodes a haemoglobin-like protein in Escherichia coli K-12. Mol Gen Genet. 1991 Apr;226(1-2):49–58. [PubMed]
  • Vinogradov SN, Walz DA, Pohajdak B, Moens L, Kapp OH, Suzuki T, Trotman CN. Adventitious variability? The amino acid sequences of nonvertebrate globins. Comp Biochem Physiol B. 1993 Sep;106(1):1–26. [PubMed]
  • Wakabayashi S, Matsubara H, Webster DA. Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla. Nature. 322(6078):481–483. [PubMed]
  • Warshel A, Naray-Szabo G, Sussman F, Hwang JK. How do serine proteases really work? Biochemistry. 1989 May 2;28(9):3629–3637. [PubMed]
  • Xia ZX, Mathews FS. Molecular structure of flavocytochrome b2 at 2.4 A resolution. J Mol Biol. 1990 Apr 20;212(4):837–863. [PubMed]
  • Zhu H, Riggs AF. Yeast flavohemoglobin is an ancient protein related to globins and a reductase family. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):5015–5019. [PMC free article] [PubMed]

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