Structure of papain refined at 1.65 Å resolution

Kamphuis, I.G.; Kalk, K.H.; Swarte, M.B.A.; Drenth, Jan

doi:10.1016/0022-2836(84)90467-4

Cited by 521 publications

(350 citation statements)

References 35 publications

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“…7 This characteristic makes Asp57 unique among the other candidates for electrostatic modulators (charge compensation is achieved for Glu35 by Lys17 and Lys174, for Glu50 by Arg83, for Glu52 by His81 and for Asp55 by Arg96) and reinforces the hypothesis that it can be an important residue in the electrostatic switch mechanism.…”

Section: Electrostatic Switch Mechanism and Possible Electrostatic Mosupporting

confidence: 55%

“…This conclusion is corroborated by experimental results and analysis presented in the literature, which indicate that the active site structural integrity is an important factor to the catalytic efficiency of papain. The papain structural characteristics that are thought to give some conformational rigidity to the active site region are as follows: (1) the presence of a network of interface interactions between the two papain domains that makes large domain movements unlikely 7,40 ; and (2) the presence of important hydrogen-bonding interactions involving the side-chains of Gln19, Asn175, and Asp158. 38,39,41 Theoretical studies made by Rullmann et al 34 and Dijkman et al 32 show that the ion pair formation is very sensitive to the distance and the relative geometry of the Cys25 and His159 side chains.…”

Section: The Net Electric Field Highly Aligned In the (Cys25)-sg3(hismentioning

confidence: 99%

“…Members of the papain family are implicated in a variety of physiologic and pathologic processes in eukaryotic organisms and are considered as important molecular targets in the development of chemotherapy against parasitic diseases (e.g., Chagas' disease, malaria) that affect millions of people around the world. 4 -6 One of the major structural characteristics of papain, 1,7 shared by the other members of the family, is the presence of two interacting domains delimiting a deep active site cleft. The essential catalytic residues in the active site consist of a cysteine (Cys25) located in an alpha helix in the L-domain and a histidine (His159) located in an antiparallel beta sheet structure in the opposite domain of the enzyme.…”

Section: Introductionmentioning

confidence: 99%

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Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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Section: Electrostatic Switch Mechanism and Possible Electrostatic Mosupporting

confidence: 55%

Section: The Net Electric Field Highly Aligned In the (Cys25)-sg3(hismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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“…The papain [7], actinidin [8], human liver cathepsin B [9], caricain D158E mutant complexed with E-64 was concentrated to approx. 13 [10], cruzain [11] and glycyl endopeptidase [12].…”

Section: Preparation and Crystallizationmentioning

confidence: 99%

Crystal structure of a caricain D158E mutant in complex with E‐64

et al. 1996

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'similar' hydrogen bonds to the Asp but the Glu could not. Abstract The structure of the D158E mutant of caricain (previously known as papaya protease omega) in complex withThese authors clearly consider that Asn could fit neatly into E-64 has been determined at 2.0 A resolution (overall R factor the unperturbed structure whilst the Glu side chain is too long 19.3%). The structure reveals that the substituted glutamate to fit. Taylor et al. [19] report the effect of substituting Ala, makes the same pattern of hydrogen bonds as the aspartate in Asn and Glu for Asp-158 in caricain and highlight the potennative caricain. This was not anticipated since in the native tial multiple ionizations involved in activity. The kcJKm valstructure there is insufficient room to accommodate the ues for the caricain mutants rank Asp > Glu >Asn > Ala. glutamate side chain. The glutamate is accommodated in the This suggests that for caricain the Glu-158 mutant is the mutant by a local expansion of the structure demonstrating that most similar in structure as it has the highest activity. Clearly, small structural changes are responsible for the change in the same hydrogen bonds could be made by the glutamate if it activity, could be accommodated within the structure.To establish the position of the glutamate side chain at Key words: Kinetically influential mutant; Cysteine protease; Site directed mutagenesis; X-ray crystallography; position 158 in caricain we have determined the structure by Enzyme-inhibitor complex X-ray crystallography. We discuss this structure and activity, and the implications for understanding the effect of mutations at the corresponding position in papain.

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“…The other subtilisin-like proteases in the database ranked 15, 16, 18, and 19. Strikingly, actinidin (2act;Baker 8c Dodson, 1980) and papain (9pap; Kamphuis et al, 1984), 2 sulfhydryl proteases, also rank very high in the scan with chymotrypsin. In Table 1 (and Fig.…”

Section: A Serine Protease Scanmentioning

confidence: 99%

Three‐dimensional, sequence order‐independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding

et al. 1994

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We have recently developed a fast approach to comparisons of 3-dimensional structures. Our method is unique, treating protein structures as collections of unconnected points (atoms) in space. It is completely independent of the amino acid sequence order. It is unconstrained by insertions, deletions, and chain directionality. It matches single, isolated amino acids between 2 different structures strictly by their spatial positioning regardless of their relative sequential position in the amino acid chain. It automatically detects a recurring 3D motif in protein molecules. No predefinition of the motif is required. The motif can be either in the interior of the proteins or on their surfaces. In this work, we describe an enhancement over our previously developed technique, which considerably reduces the complexity of the algorithm. This results in an extremely fast technique. A typical pairwise comparison of 2 protein molecules requires less than 3 s on a workstation. We have scanned the structural database with dozens of probes, successfully detecting structures that are similar to the probe. To illustrate the power of this method, we compare the structure of a trypsin-like serine protease against the structural database. Besides detecting homologous trypsin-like proteases, we automatically obtain 3D, sequence order-independent, active-site similarities with subtilisin-like and sulfhydryl proteases. These similarities equivalence isolated residues, not conserving the linear order of the amino acids in the chains. The active-site similarities are well known and have been detected by manually inspecting the structures in a time-consuming, laborious procedure. This is the first time such equivalences are obtained automatically from the comparison of full structures. The far-reaching advantages and the implications of our novel algorithm to studies of protein folding, to evolution, and to searches for pharmacophoric patterns are discussed.Keywords: computer vision; protease active sites; protein database structural comparison; protein folding; 3D protein motifsWe have recently developed an extremely fast, template-free, sequence order-independent technique for the comparisons of the 3-dimensional structures of proteins. There are 3 novel aspects in our method. First, we compare the 3D structures of proteins (or any biological macromolecule) completely regardless of the order of the residues in the chain. This allows us to detect similarities between protein molecules, whether these are on their surfaces or in their interior. Our computer vision-based algorithm views atoms as collections of unconnected points in space.Reprint requests to: Ruth Nussinov, Building 469, Room 151, NCI-FCRF, Frederick, Maryland 21702; e-mail: ruthn@fcrfvl.ncifcrf.gov. This truly 3D approach overcomes a major limitation inherent in other structural comparison techniques which require that the linear order of the amino acid sequences be conserved (e.g., Matthews & Rossmann, 1985). Although some techniques overcome the insertion/del...

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Structure of papain refined at 1.65 Å resolution

Cited by 521 publications

References 35 publications

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Crystal structure of a caricain D158E mutant in complex with E‐64

Three‐dimensional, sequence order‐independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding

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