Nicolas A

General

Full name : Nicolas Anne

First name : Anne

Mail : Bijvoet Center of Biomolecular Research, Dept. of Crystal and Structural Chemistry, Padualaan 8, 3584 CH Utrecht

Zip Code :

City :

Country : The Netherlands

Email : a.nicolas@chem.ruu.nl

Phone : 31-30-253-2869

Fax : 31-30-253-3940

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References (10)

Title : Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif - Silman_2021_Protein.Sci_30_966
Author(s) : Silman I , Shnyrov VL , Ashani Y , Roth E , Nicolas A , Sussman JL , Weiner L
Ref : Protein Science , 30 :966 , 2021
Abstract : Stabilization of Torpedo californica acetylcholinesterase by the divalent cations Ca(+2) , Mg(+2) and Mn(+2) was investigated. All three substantially protect the enzyme from thermal inactivation. Electron paramagnetic resonance revealed one high-affinity binding site for Mn(+2) and several much weaker sites. Differential scanning calorimetry showed a single irreversible thermal transition. All three cations raise both the temperature of the transition and the activation energy, with the transition becoming more cooperative. The crystal structures of the Ca(+2) and Mg(+2) complexes with Torpedo acetylcholinesterase were solved. A principal binding site was identified. In both cases, it consists of four aspartates (a 4D motif), within which the divalent ion is embedded, together with several waters molecules. It makes direct contact with two of the aspartates, and indirect contact, via waters, with the other two. The 4D motif has been identified in 31 acetylcholinesterase sequences and 28 butyrylcholinesterase sequences. Zebrafish acetylcholinesterase also contains the 4D motif; it, too, is stabilized by divalent metal ions. The ASSAM server retrieved 200 other proteins that display the 4D motif, in many of which it is occupied by a divalent cation. It is a very versatile motif, since, even though tightly conserved in terms of rmsd values, it can contain from one to as many as three divalent metal ions, together with a variable number of waters. This novel motif, which binds primarily divalent metal ions, is shared by a broad repertoire of proteins. This article is protected by copyright. All rights reserved.
ESTHER : Silman_2021_Protein.Sci_30_966
PubMedSearch : Silman_2021_Protein.Sci_30_966
PubMedID: 33686648
Gene_locus related to this paper: torca-ACHE

Title : Histochemical method for characterization of enzyme crystals: application to crystals of Torpedo californica acetylcholinesterase - Nicolas_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1348
Author(s) : Nicolas A , Ferron F , Toker L , Sussman JL , Silman I
Ref : Acta Crystallographica D Biol Crystallogr , 57 :1348 , 2001
Abstract : Histochemical methods are employed to detect and localize a wide range of enzymes. Even though protein crystallographers do not commonly use this technique, the extensively used colorimetric reaction of Karnovsky was successfully adapted for easy and quick identification of acetylcholinesterase crystals. The method relies on the reduction of ferricyanide to ferrocyanide by thiocholine, released from acetylthiocholine by enzymatic hydrolysis, followed by formation of a cupric ferrocyanide precipitate, and allows rapid differentiation between salt and enzyme crystals and between native and inhibited crystals of the enzyme.
ESTHER : Nicolas_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1348
PubMedSearch : Nicolas_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1348
PubMedID: 11526341

Title : Alternative Crystal Forms of Torpedo Californica Acetylcholinesterase -
Author(s) : Raves ML , Greenblatt HM , Kryger G , Nicolas A , Ravelli RB , Harel M , Kroon J , Silman I , Sussman JL
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :372 , 1998
PubMedID:

Title : Activity of Torpedo Californica Acetylcholinesterase in the Crystalline State -
Author(s) : Nicolas A , Millard CB , Raves ML , Ravelli RB , Kroon J , Silman I , Sussman JL
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :230 , 1998
PubMedID:

Title : Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis - Longhi_1997_J.Mol.Biol_268_779
Author(s) : Longhi S , Czjzek M , Lamzin V , Nicolas A , Cambillau C
Ref : Journal of Molecular Biology , 268 :779 , 1997
Abstract : X-ray data have been recorded to 1.0 A resolution from a crystal of Fusarium solani cutinase using synchrotron radiation and an imaging-plate scanner. The anisotropic treatment of thermal motion led to a fivefold increase in accuracy and to a considerable quality improvement in the electron density maps with respect to an intermediate isotropic model. The final model has an R-factor of 9.4%, with a mean coordinate error of 0.021 A, as estimated from inversion of the least-squares matrix. The availability of an accurate structure at atomic resolution and of meaningful estimates of the errors in its atomic parameters, allowed an extensive analysis of several stereochemical parameters, such as peptide planarity, main-chain and some side-chain bond distances. The hydrogen atoms could be clearly identified in the electron density, thus providing unambiguous evidence on the protonation state of the catalytic histidine residue. The atomic resolution revealed an appreciable extent of flexibility in the cutinase active site, which might be correlated with a possible adaptation to different substrates. The anisotropic treatment of thermal factors provided insights into the anisotropic nature of motions. The analysis of these motions in the two loops delimiting the catalytic crevice pointed out a "breath-like" movement in the substrate binding region of cutinase.
ESTHER : Longhi_1997_J.Mol.Biol_268_779
PubMedSearch : Longhi_1997_J.Mol.Biol_268_779
PubMedID: 9175860
Gene_locus related to this paper: fusso-cutas , orysa-LPL1

Title : Acyl glycerol hydrolases: inhibitors, interface and catalysis - Cambillau_1996_Curr.Opin.Struct.Biol_6_449
Author(s) : Cambillau C , Longhi S , Nicolas A , Martinez C
Ref : Current Opinion in Structural Biology , 6 :449 , 1996
Abstract : The last five years have witnessed the solution of a large number of lipase structures, which has led, among other insights, to the structural interpretation of the interfacial activation phenomenon in terms of 'lid' opening. This interpretation has been extended this year to include phospholipase A2. Recent structural studies on lipases have provided data on the detailed mechanisms underlying the behaviour of lipases: how they bind to inhibitors or substrates, and what interactions occur between their hydrophobic face and hydrophobic molecules, for example. In addition, studies on cutinase point mutants have shed some light on the role of the oxyanion hole in lipolytic catalysis.
ESTHER : Cambillau_1996_Curr.Opin.Struct.Biol_6_449
PubMedSearch : Cambillau_1996_Curr.Opin.Struct.Biol_6_449
PubMedID: 8794161

Title : Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants - Longhi_1996_Proteins_26_442
Author(s) : Longhi S , Nicolas A , Creveld L , Egmond M , Verrips CT , de Vlieg J , Martinez C , Cambillau C
Ref : Proteins , 26 :442 , 1996
Abstract : In characterizing mutants and covalently inhibited complexes of Fusarium solani cutinase, which is a 197-residue lipolytic enzyme, 34 variant structures, crystallizing in 8 different crystal forms, have been determined, mostly at high resolution. Taking advantage of this considerable body of information, a structural comparative analysis was carried out to investigate the dynamics of cutinase. Surface loops were identified as the major flexible protein regions, particularly those forming the active-site groove, whereas the elements constituting the protein scaffold were found to retain the same conformation in all the cutinase variants studied. Flexibility turned out to be correlated with thermal motion. With a given crystal packing environment, a high flexibility turned out to be correlated with a low involvement in crystal packing contacts. The high degree of crystal polymorphism, which allowed different conformations with similar energy to be detected, made it possible to identify motions which would have remained unidentified if only a single crystal form had been available. Fairly good agreement was found to exist between the data obtained from the structural comparison and those from a molecular dynamics (MD) simulation carried out on the native enzyme. The crystallographic approach used in this study turned out to be a suitable tool for investigating cutinase dynamics. Because of the availability of a set of closely related proteins in different crystal environments, the intrinsic drawback of a crystallographic approach was bypassed. By combining several static pictures, the dynamics of the protein could be monitored much more realistically than what can be achieved on the basis of static pictures alone.
ESTHER : Longhi_1996_Proteins_26_442
PubMedSearch : Longhi_1996_Proteins_26_442
PubMedID: 8990497
Gene_locus related to this paper: fusso-cutas

Title : Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state - Nicolas_1996_Biochemistry_35_398
Author(s) : Nicolas A , Egmond M , Verrips CT , de Vlieg J , Longhi S , Cambillau C , Martinez C
Ref : Biochemistry , 35 :398 , 1996
Abstract : Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.
ESTHER : Nicolas_1996_Biochemistry_35_398
PubMedSearch : Nicolas_1996_Biochemistry_35_398
PubMedID: 8555209
Gene_locus related to this paper: fusso-cutas

Title : Cutinase, a lipolytic enzyme with a preformed oxyanion hole - Martinez_1994_Biochemistry_33_83
Author(s) : Martinez C , Nicolas A , van Tilbeurgh H , Egloff MP , Cudrey C , Verger R , Cambillau C
Ref : Biochemistry , 33 :83 , 1994
Abstract : Cutinases, a group of cutin degrading enzymes with molecular masses of around 22-25 kDa (Kolattukudy, 1984), are also able to efficiently hydrolyse triglycerides (De Geus et al., 1989; Lauwereys et al., 1991), but without exhibiting the interfacial activation phenomenom (Sarda et al., 1958). They belong to a class of proteins with a common structural framework, called the alpha/beta hydrolase fold (Martinez et al., 1992; Ollis et al., 1992). We describe herein the structure of cutinase covalently inhibited by diethyl-p-nitrophenyl phosphate (E600) and refined at 1.9-A resolution. Contrary to what has previously been reported with lipases (Brzozowski et al., 1991; Derewenda et al., 1992; Van Tilbeurgh et al., 1993), no significant structural rearrangement was observed here in cutinase upon the inhibitor binding. Moreover, the structure of the active site machinery, consisting of a catalytic triad (S120, H188, D175) and an oxyanion hole (Q121 and S42), was found to be identical to that of the native enzyme, whereas the oxyanion hole of Rhizomucor lipase (Brzozowski et al., 1991; Derewenda et al., 1992), like that of pancreatic lipase (van Tilbeurgh et al., 1993), is formed only upon enzyme-ligand complex formation. The fact that cutinase does not display interfacial activation cannot therefore only be due to the absence of a lid but might also be attributable to the presence of a preformed oxyanion hole.
ESTHER : Martinez_1994_Biochemistry_33_83
PubMedSearch : Martinez_1994_Biochemistry_33_83
PubMedID: 8286366
Gene_locus related to this paper: fusso-cutas , orysa-LPL1

Title : The MET2 gene of Saccharomyces cerevisiae: molecular cloning and nucleotide sequence - Langin_1986_Gene_49_283
Author(s) : Langin T , Faugeron G , Goyon C , Nicolas A , Rossignol JL
Ref : Gene , 49 :283 , 1986
Abstract : A 5.1-kb DNA fragment from Saccharomyces cerevisiae, which complements a yeast met2 mutant strain, has been cloned. This fragment contains the wild-type MET2 gene which codes for the homoserine O-transacetylase, one of the methionine biosynthetic enzymes. The presence of the MET2 gene has been shown by integrative transformation experiments and genetic analyses of the resulting transformants. The complete nucleotide sequence of a 2826-bp DNA fragment carrying the MET2 gene has been determined. The sequence contains one major open reading frame of 438 codons, giving a calculated Mr of 48,370 for the encoded protein. We have identified the transcriptional product of the MET2 gene and estimated its size at 1650 nucleotides.
ESTHER : Langin_1986_Gene_49_283
PubMedSearch : Langin_1986_Gene_49_283
PubMedID: 3552887
Gene_locus related to this paper: yeast-met2