Research Programmes
Structural & Computational Biology
Structural biology of macromolecular aggregates
Ignasi Fita
Group Leader
Professor (IBMB-CSIC)
Office Tel : +34 93 40 34949
e-mail : ignasi.fita
irbbarcelona.org
Background
During the last fifteen years our research has focused on the structure-function relationships of a diversity of proteins and macromolecular complexes directly involved in pathological processes. The systems studied, with over a hundred peer-reviewed publications, range from a number of small protein kinase domains to several intact RNA viruses and in complex with their cellular receptors. To perform our activities, we use mainly X-ray crystallography, often complemented with other techniques including, in particular, mass spectrometry and high resolution cryo-electron microscopy.
Research Interests
Our general goal is first to determine the three-dimensional organization of a number of molecular systems, and second, to use these data as a framework to examine the biochemical and biological processes in which these molecular systems participate. The development of methodologies required by some of these studies has also been an objective in itself.
Research Lines
At present our main lines of research are:
Enzymes related with Oxidative Stress
a) Mono-functional Catalases,
b) Bifunctional Catalases-Peroxidases,
c) Peroxidases (in particular mammalian peroxidases) and
d) Oxygenases.
Membrane bound proteins
a) Amino-acid transporters and
b) Virulence factors (in particular in Mycoplasmas)
Energetics of protein conformations
More info
Structural biology of macromolecular aggregates
Selected publications
Crystal structure of an archaeal glycogen synthase: Insights intooligomerization and substrate binding of eukaryotic glycogen synthases
Horcajada C, Guinovart J, Fita I and Ferrer JC
J Biol Chem (281), 2923-31 (2006)
Oxygen Binding to Catalase-Peroxidase
Vidossich P, Carpena X, Loewen PC, Fita I and Rovira C
J Phys Chem Lett, 2 (3), 196-200 (2011)
Thirty years of heme catalases structural biology
Díaz A, Loewen PC, Fita I and Carpena X.
Arch Biochem Biophys (2011)
Processivity and subcellular localization of glycogen synthase depend on a non-catalytic high affinity glycogen-binding site
Díaz A, Martínez-Pons C, Fita I, Ferrer JC and Guinovart JJ.
J Biol Chem, 21 (286), 18505-14 (2011)
Modulation of heme orientation and binding by a single residue in catalase HPII of Escherichia coli
Jha V, Louis S, Chelikani P, Carpena X, Donald LJ, Fita I and Loewen PC.
Biochemistry, 12 (50), 2101-10 (2011)
Molecular basis of substrate-induced permeation by an amino acid antiporter
Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL and Palacín M.
Proc Natl Acad Sci U S A, 10 (108), 3935-40 (2011)
Re-engineering specificity in 1,3-1, 4-β-glucanase to accept branched xyloglucan substrates
Addington T, Calisto B, Alfonso-Prieto M, Rovira C, Fita I and Planas A.
Proteins, 2 (79), 365-75 (2011)
The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations
Vidossich P, Alfonso-Prieto M, Carpena X, Fita I, Loewen PC and Rovira C.
Arch Biochem Biophys, 1 (500), 37-44 (2010)
Substrate binding and catalysis in carbamate kinase ascertained by crystallographic and site-directed mutagenesis studies: movements and significance of a unique globular subdomain of this key enzyme for fermentative ATP production in bacteria
Ramón-Maiques S, Marina A, Guinot A, Gil-Ortiz F, Uriarte M, Fita I and Rubio V.
J Mol Biol, 5 (397), 1261-75 (2010)
The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP
Querol-Audí J, Casañas A, Usón I, Luque D, Castón JR, Fita I and Verdaguer N.
Embo J, 21 (28), 3450-7 (2009)
Essential role of proximal histidine-asparagine interaction in mammalian peroxidases
Carpena X, Vidossich P, Schroettner K, Calisto BM, Banerjee S, Stampler J, Soudi M, Furtmüller PG, Rovira C, Fita I and Obinger C.
J Biol Chem, 38 (284), 25929-37 (2009)
Three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase PIG3
Porté S, Valencia E, Yakovtseva EA, Borràs E, Shafqat N, Debreczeny JE, Pike AC, Oppermann U, Farrés J, Fita I and Parés X.
J Biol Chem, 25 (284), 17194-205 (2009)
Structural and mechanistic insights into the association of PKCalpha-C2 domain to PtdIns(4,5)P2
Guerrero-Valero M, Ferrer-Orta C, Querol-Audí J, Marin-Vicente C, Fita I, Gómez-Fernández JC, Verdaguer N and Corbalán-García S.
Proc Natl Acad Sci U S A, 16 (106), 6603-7 (2009)
Arginine and nitrogen storage
Llácer JL, Fita I and Rubio V
Curr Opin Struct Biol, 6 (18), 673-81 (2008)
Electronic state of the molecular oxygen released by catalase
Alfonso-Prieto M, Vidossich P, Rodri_guez-Fortea A, Carpena X, Fita I, Loewen PC and Rovira C
J Phys Chem A, 50 (112), 12843-48 (2008)
Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases
Brucet M, Querol-Audí J, Bertlik K, Lloberas J, Fita I and Celada A
Protein Sci, 12 (17), 2059-69 (2008)
RhaU of Rhizobium leguminosarum is a rhamnose mutarotase
Richardson JS, Carpena X, Switala J, Perez-Luque R, Donald LJ, Loewen PC and Oresnik IJ
J Bacteriol, 8 (190), 2903-10 (2008)
Aldo-keto reductases from the AKR1B subfamily: retinoid specificity and control of cellular retinoic acid levels
Ruiz FX, Gallego O, Ardèvol A, Moro A, Domínguez M, Alvarez S, Alvarez R, de Lera AR, Rovira C, Fita I, Parés X and Farrés J
Chem Biol Interact, 39141 (178), 171-77 (2008)
Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition
Querol-Audí J, Konecsni T, Pous J, Carugo O, Fita I, Verdaguer N and Blaas D
FEBS Lett, 1 (583), 235-40 (2008)
Structural basis for the high all-trans-retinaldehyde reductase activity of the tumor marker AKR1B10
Gallego O, Ruiz FX, Ardevol A, Domínguez M, lvarez R, de Lera AR, Rovira C, Farres J, Fita I and Pares X
Proc Natl Acad Sci USA (104), 20764-69 (2007)
Versatility of the electronic structure of compound I in catalase-peroxidases
Vidossich P, Alfonso-Prieto M, Carpena X, Loewen PC, Fita I and Rovira C
J Am Chem Soc (129), 13436-46 (2007)
The crystal structure of the complex of PII and acetylglutamate kinase reveals how PII controls the storage of nitrogen as arginine
Llácer JL, Contreras A, Forchhammer K, Marco-Marín C, Gil-Ortiz F, Maldonado R, Fita I and Rubio V
Proc Natl Acad Sci U S A (104), 17644-49 (2007)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane
Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Usón I, Zorzano A, Fernández-Recio J, Orozco M, Lizarbe MA, Fita I and Palacín M.
J Biol Chem, 43 (282), 31444-52 (2007)
Biosynthesis of isoprenoids in plants: structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes
Calisto BM, Perez-Gil J, Bergua M, Querol-Audi J, Fita I and Imperial S
Protein Sci (9), 2082-88 (2007)
Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains
Brucet M, Querol-Audí J, Serra M, Ramirez-Espain X, Bertlik K, Ruiz L, Lloberas J, Macias MJ, Fita I and Celada A
J Biol Chem, 19 (282), 1454 (2007)
A novel two-domain architecture within the amino acid kinase enzyme family revealed by the crystal structure of Escherichia coli glutamate 5-kinase
Marco-Marín C, Gil-Ortiz F, Pérez-Arellano I, Cervera J, Fita I and Rubio V
J Mol Biol (367), 1431-46 (2007)
The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations
Alfonso-Prieto M, Borovik A, Carpena X, Murshudov G, Melik-Adamyan W, Fita I, Rovira C and Loewen PC
J Am Chem Soc (129), 4193-05 (2007)
Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei
Deemagarn T, Wiseman B, Carpena X, Ivancich A, Fita I and Loewen PC
Proteins (66), 219-28 (2007)
Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium
Calisto BM, Pich OQ, Piñol J, Fita I, Querol E and Carpena X
J Mol Biol, 351 (4), 749-762 (2005)
Preliminary analysis of two and three dimensional crystals of vault ribonucleoprotein particles
Querol J, Perez-Luque R, Fita I, Lopez C, Gastón JR, Carrascosa JL and Verdaguer N
J Struct Biol, 151, 111-115 (2005)
A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases
Carpena X, Wiseman B, Deemagarn T, Singh R, Switala J, Ivancich A, Fita I and Loewen PC
EMBO Rep, 6 (12), 1156-1162 (2005)
Structural characterization of the Ser324Thr variant of the catalase-peroxidase (KatG) from Burkholderia pseudomallei
Deemagarn T, Carpena X, Singh R, Wiseman B, Fita I and Loewen PC
J Mol Biol, 345 (1), 21-28 (2005)
A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
Rovira C, Alfonso-Prieto M, Biarnes X, Carpena X, Fita I and Loewen PC
Chem Phys, 323, 129-137 (2005)
Characterization of a large subunit catalase truncated by proteolytic cleavage
Chelikani P, Carpena X, Pérez-Luque R, Donald LJ, Duckworth HW, Switala J, Fita I and Loewen PC
Biochemistry, 44 (15), 5597-5605 (2005)
Structural plasticity in alcohol dehydrogenase: How an NADP (H)-dependent enzyme becomes specific for NAD(H)
Rosell A, Valencia E, Borras E, Ochoa WF, Fita I, Pares X and Farres J
Enzymol Mol Biol Carbonyl Metab, 12, 181-189 (2005)
X-ray crystallography of rhinovirus-receptor complexes
Querol J, Fita I and Verdaguer N
Crystallogr Rev, 11, 73-81 (2005)
Catalase-peroxidases (KatG) exhibit NADH oxidase activity
Singh R, Wiseman B, Deemagarn T, Donald LJ, Duckworth HW, Carpena X, Fita I and Loewen PC
J Biol Chem, 279 (41), 43098-43106 (2004)
Apo and Holo structures of an NADPH-dependent cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae
Valencia E, Larroy C, Ochoa WF, Parés X, Fita I and Biosca JA
J Mol Biol, 341 (4), 1049-1062 (2004)
X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein
Verdaguer N, Fita I, Reithmayer M, Moser R and Blaas D
Nat Struct Mol Biol, 11 (5), 429-434 (2004)
An electrical potential in the access channel of catalases enhances catalysis
Chelikani P, Carpena X, Fita I and Loewen PC
J Biol Chem, 278 (33), 31290-31296 (2003)
Characterization of the catalase-peroxidase KatG from Burkholderia pseudomallei by mass spectrometry
Donald LJ, Krokhin OV, Duckworth HW, Wiseman B, Deemagarn T, Singh R, Switala J, Carpena X, Fita I and Loewen PC
J Biol Chem, 278 (37), 35687-35692 (2003)
The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic
Gil-Ortiz F, Ramón-Maiques S, Fita I and Rubio V
J Mol Biol, 331 (1), 231-244 (2003)
Complete reversal of coenzyme specificity by concerted mutation of three consecutive residues in alcohol dehydrogenase
Rosell A, Valencia E, Ochoa WF, Fita I, Pares X and Farres J
J Biol Chem, 278 (42), 40573-40580 (2003)
Crystal structure of the vertebrate NADP(H)-dependent alcohol dehydrogenase (ADH8)
Rosell A, Valencia E, Parés X, Fita I, Farrés J and Ochoa WF
J Mol Biol, 330 (1), 75-85 (2003)
Structure of swine vesicular disease virus: mapping of changes occurring during adaptation of human coxsackie B5 virus to infect swine
Verdaguer N, Jimenez-Clavero MA, Fita I and Ley V
J Virol, 77 (18), 9780-9789 (2003)
Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution
Carpena X, Loprasert S, Mongkolsuk S, Switala J, Loewen PC and Fita I
J Mol Biol, 327 (2), 475-489 (2003)
Structural biology of macromolecular aggregates
Ignasi Fita
Group Leader
Professor (IBMB-CSIC)
Office Tel : +34 93 40 34949
e-mail : ignasi.fita
irbbarcelona.org
Postdoctoral Fellows
Xavi Carpena
tel +34 93 40 34956
e-mail: xavier.carpena
irbbarcelona.org
PhD Students
David Aparicio
tel +34 93 40 34956
e-mail: david.aparicio
irbbarcelona.org
Luca Martinelli
tel +34 93 40 34956
e-mail: luca.martinelli
irbbarcelona.org
Maria Adell
tel +34 93 40 34956
e-mail: maria.adell
irbbarcelona.org
Lab Technicians
Mª Queralt García
tel +34 93 40 34956
e-mail: maria.garcia
irbbarcelona.org
Structural biology of macromolecular aggregates
- 11 April 2011
Barcelona Visió
X-Rays against the bacterium that causes tuberculosis - 19 January 2011
Investigación y Ciencia
The common cold virus - 14 April 2010
El País
Biological challenges for a synchrotron - 26 October 2009
Global Talent
Vèncer la destresa del bacteri de la tuberculosi - 19 October 2009
Global Talent
El IRB Barcelona participa en un proyecto europeo contra la tuberculosis








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