Fast rigid-body refinement for molecular-replacement techniques

Castellano, E. E.; Oliva, Glaucius; Navaza, Jorge

doi:10.1107/s0021889891012773

Cited by 60 publications

(38 citation statements)

References 5 publications

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“…An unambiguous single solution for the rotation and translation functions was obtained for all proteins. These solutions were refined by the fast rigid body refinement program FITING (43). The models were subjected to alternate cycles of conjugate gradient refinement with the program X-PLOR (44) and manual model building with the software package O (45).…”

Section: Methodsmentioning

confidence: 99%

Role of a Cluster of Hydrophobic Residues Near the FAD Cofactor in Anabaena PCC 7119 Ferredoxin-NADP+Reductase for Optimal Complex Formation and Electron Transfer to Ferredoxin

Martínez‐Júlvez

Nogués

Faro

et al. 2001

Journal of Biological Chemistry

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In the ferredoxin-NADP؉ reductase (FNR)/ferredoxin (Fd) system, an aromatic amino acid residue on the surface of Anabaena Fd, Phe-65, has been shown to be essential for the electron transfer (ET) reaction. We have investigated further the role of hydrophobic interactions in complex stabilization and ET between these proteins by replacing three hydrophobic residues, Leu-76, Leu-78, and Val-136, situated on the FNR surface in the vicinity of its FAD cofactor. Whereas neither the ability of FNR to accept electrons from NADPH nor its structure appears to be affected by the introduced mutations, different behaviors with Fd are observed. Thus, the ET interaction with Fd is almost completely lost upon introduction of negatively charged side chains. In contrast, only subtle changes are observed upon conservative replacement. Introduction of Ser residues produces relatively sizable alterations of the FAD redox potential, which can explain the modified behavior of these mutants. The introduction of bulky aromatic side chains appears to produce rearrangements of the side chains at the FNR/Fd interaction surface. Thus, subtle changes in the hydrophobic patch influence the rates of ET to and from Fd by altering the binding constants and the FAD redox potentials, indicating that these residues are especially important in the binding and orientation of Fd for efficient ET. These results are consistent with the structure reported for the Anabaena FNR⅐Fd complex.There are many examples throughout biology in which physiological function involves protein-protein interaction. Important illustrations of this are the reactions that occur between proteins in the ET 1 chains participating in photosynthesis, respiration, nitrogen fixation, and cytochrome P450 hydroxylations. In all of these cases, specific recognition and binding occur between the donor and the acceptor proteins. Although the structural parameters that determine such recognition are not fully understood, it is widely accepted that a transient complex between the two proteins must be formed and that the mutual orientation of the two proteins within the complex determines the rate of the ET reaction. For the last 10 years a large effort has gone into the study of the interaction between two ET proteins participating in the metabolism of the cyanobacterium Anabaena PCC 7119, ferredoxin (Fd), and ferredoxin-NADP ϩ reductase (FNR) (1-18). During photosynthesis, FNR catalyzes the transfer of electrons from the one-electron carrier Fd to the two-electron acceptor NADP ϩ to produce NADPH (19). Both proteins from Anabaena have been cloned and expressed in Escherichia coli (20 -22), and their high resolution x-ray structures have been determined (23,24). All of the biochemical and structural information available on these proteins indicates that Fd binds in a concave cavity around the FAD group of the reductase (2, 25), and this hypothesis has been strongly supported by the recent x-ray structures reported for the complex formed by Fd and FNR, either with the Anabaena or the maiz...

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Section: Methodsmentioning

confidence: 99%

Role of a Cluster of Hydrophobic Residues Near the FAD Cofactor in Anabaena PCC 7119 Ferredoxin-NADP+Reductase for Optimal Complex Formation and Electron Transfer to Ferredoxin

Martínez‐Júlvez

Nogués

Faro

et al. 2001

Journal of Biological Chemistry

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“…The apo HpSK structure was solved by molecular replacement with the program AMoRe (33), using the structure of CjSK (PDB code, 1VIA) as the search model. Rotation and translation functions followed by the rigid body refinement procedure of AMoRe (4,33) were carried out using data from 8-to 4-Å resolution and yielded one outstanding solution (fractional coordinates, x ϭ 0.136, y ϭ 0.682, and z ϭ 0.078). Crystallographic refinement was carried out using the maximum-likelihood target function embedded in program REFMAC5 (32) and coupled to ARP/wARP (22).…”

Section: Methodsmentioning

confidence: 99%

Structural Basis for Shikimate-Binding Specificity of Helicobacter pylori Shikimate Kinase

2005

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Shikimate kinase (EC 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP. As the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, but not mammals, shikimate kinase represents an attractive target for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here, we report the 1.8-Å crystal structure of Helicobacter pylori shikimate kinase (HpSK). The crystal structure shows a three-layer alpha/beta fold consisting of a central sheet of five parallel ␤-strands flanked by seven ␣-helices. An HpSK-shikimate-PO 4 complex was also determined and refined to 2.3 Å, revealing induced-fit movement from an open to a closed form on substrate binding. Shikimate is located above a short 3 10 helix formed by a strictly conserved motif (GGGXV) after ␤ 3 . Moreover, several highly conserved charged residues including Asp33 (in a conserved DT/SD motif), Arg57, and Arg132 (interacting with shikimate) are identified, guiding the development of novel inhibitors of shikimate kinase.

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“…CC I as a function of T m . The re®nement of the positional variables is performed with the fast rigid-body re®nement program FITING (Castellano et al, 1992). These fast functions will be described in the following section.…”

Section: Strategymentioning

confidence: 99%

Implementation of molecular replacement in AMoRe

Navaza

2001

Acta Crystallogr D Biol Crystallogr

636

450

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An account is given of the molecular replacement method as implemented in the package AMoRe. The overall strategy of the method is presented and the main functions used in the package are described. The most important features of AMoRe are the quality of the fast rotation and translation functions and the facility of multiple inputs to translation and rigid-body re®nement functions, which allow for a fast multiple exploration of crystal con®gurations with a high level of automation.

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Fast rigid-body refinement for molecular-replacement techniques

Cited by 60 publications

References 5 publications

Role of a Cluster of Hydrophobic Residues Near the FAD Cofactor in Anabaena PCC 7119 Ferredoxin-NADP+Reductase for Optimal Complex Formation and Electron Transfer to Ferredoxin

Role of a Cluster of Hydrophobic Residues Near the FAD Cofactor in Anabaena PCC 7119 Ferredoxin-NADP+Reductase for Optimal Complex Formation and Electron Transfer to Ferredoxin

Structural Basis for Shikimate-Binding Specificity of Helicobacter pylori Shikimate Kinase

Implementation of molecular replacement in AMoRe

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