The structure of α-chymotrypsin. I. The refinement of the heavy-atom isomorphous derivatives at 2.8 Å resolution

Tulinsky, A.; Mani, N. V.; Morimoto, Carl N.; Vandlen, Richard

doi:10.1107/s0567740873004437

Cited by 40 publications

(22 citation statements)

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“…Mammalian serine proteases Atomic resolution crystal structures are available for three mammalian serine proteases: chymotrypsin (13,14), trypsin (15,16), and elastase (12). Atomic coordinates for chymotrypsin (13), trypsin (15), and elastase (12) were obtained from the Atlas of Macromolecular Structure (17).…”

Section: Methods Of Building Coordinatesmentioning

confidence: 99%

Model for haptoglobin heavy chain based upon structural homology.

Greer¹

1980

Proc. Natl. Acad. Sci. U.S.A.

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ABSTRACr A model has been constructed for haptoglobin heavy chain by using the known sequence homology to the mammalian serine proteases. The three-dimensional structures for three serine proteases, chymotrypsin, trypsin, and elastase, were compared and the structural features at are conserved in all three were extracted. The haptoglobin heavy chain sequence was aligned to the sequences of the three serine proteases by maximizing sequence homology in the regions of conserved structure. The resulting alignment shows that haptoglobin heavy chain must be very closely homologous to these roteases in structure as well as in sequence. Coordinates were erived for the heavy chain by using the homologous structures. The problems associated with these coordinates are outlined and methods for solving them are indicated. The features of the haptoglobin heavy chain structure are described. Implications of the structure or the very strong interaction between this subunit and hemoglobin are discussed. Haptoglobin (Hp) is a serum glycoprotein that is present in many mammalian species (1). Its function is to form a strong and stable complex with hemoglobin that has been released from erythrocytes and foster the recycling of heme iron. Hp is a tetramer composed of two light and two heavy chains. A variety of experiments indicate that it is the Hp heavy chains (HpH) that bind a hemoglobin a# dimer during complex formation (2, 3). have reported that the sequence of HpH is clearly homologous to the mammalian serine protease family. The possibility exists, therefore, of determining the tertiary structure of HpH by fitting the sequence into the known structure for the serine proteases (7,8).Browne et al. (9) first used comparative model building from the known structure of lysozyme to predict the structure of the homologous a-lactalbumin. McLachlan and Shotton (10) applied this technique with mixed success (11) to construct a-lytic protease from the structure of elastase (12). Their model suffered from the fact that the sequence homology between the bacterial and mammalian enzymes is extremely weak.We report here the application of comparative model building to HpH. The strategy adopted was, first, to analyze the structural features common to the known serine proteases. The clear sequence homology between HpH and the other serine proteases was used to align the HpH sequence in such a way as to maximize its agreement with the structural characteristics of the serine proteases. Atomic coordinates were then constructed based upon this alignment. METHOD OF BUILDING COORDINATESMammalian serine proteases Atomic resolution crystal structures are available for three mammalian serine proteases: chymotrypsin (13, 14), trypsin (15,16), and elastase (12). Atomic coordinates for chymotrypsin (13), trypsin (15), and elastase (12) were obtained from the Atlas of Macromolecular Structure (17).The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance ...

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Section: Methods Of Building Coordinatesmentioning

confidence: 99%

Model for haptoglobin heavy chain based upon structural homology.

Greer¹

1980

Proc. Natl. Acad. Sci. U.S.A.

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Section: Twinning Correction For Pgk4 Crystalsmentioning

confidence: 99%

“…The monoclinic crystals belong to space group P21 with unit cell dimensions of a = 32.73, b = 49.09, c = 46.15 A, P = 100.6", 4 molecules per unit cell (2 molecules per asymmetric unit), and 66% protein fraction giving V, = 1.86 A3/Da (Matthews, 1968). The crystals are twinned along the c* direction in a manner similar to achymotrypsin (Tulinsky et al, 1973).…”

Section: Monoclinic Pgk4mentioning

confidence: 99%

“…In order to extract the true intensities from the reflections affected by twinning, the extent of twinning and the intensities of the reflections affected by the twinning operation must be known. Several methods have been proposed to deal with this problem (Tulinsky et al, 1973;Fisher & Sweet, 1980;Yeates, 1988). In the case of monoclinic PGK4 crystals, the overlap of the crystal and the twin is not exact everywhere, so that only a fraction of the diffraction data is adversely affected by twinning and needs to be corrected.…”

Section: Twinning Correction For Pgk4 Crystalsmentioning

confidence: 99%

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Kringle‐kringle interactions in multimer kringle structures

Padmanabhan

Ravichandran

et al. 1994

Protein Science

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The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorhombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 21 screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PC), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3,) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGKl and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.Keywords: crystal packing interactions; kringle-kringle interactions; lysine binding site interactions; 2 and 3 molecules per asymmetric unit Kringles are independent structural and functional folding domains that are 3-disulfide, triple-loop structures consisting of about 80 residues and are found in the noncatalytic regions of regulatory proteases of blood coagulation and fibrinolysis (Sottrup-Jensen et al., 1978;Patthy, 1985). It has been shown that kringles occur singly in UK-type P C activator Steffens et al., 1982), factor XI1 (McMullen & Fujikawa, 1985), and vampire bat salivary P C activator (Gardell et al., 1989), as pairs in PT (Magnusson et al., 1975) and t-PA (Pennica et al., 1983), as 4 copies in hepatocyte growth factor (Nakamura et al., 1989), and as 5 in P C (Sottrup-Jensen et al., 1978). Most striking, however, is apolipoprotein [a], with 38 kringles, 37 of which are highly homologous to PGK4 (Fig. 1) and 1 of which resembles PGK5 (McLean et al., 1987). Kringles

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“…Although three-dimensional structures of growth factors (Montelione et al, 1987;Cooke et al, 1987;Kline et al, 1990;Moyetal., 1993),kringles (de Vosetal., 1992;Mulichak et al, 1991), and serine proteases (Birktoft & Blow, 1972; Tulinsky et al, 1973;Huber et al, 1974;Stroud et al, 1974;Shotten & Watson, 1970;Sawyer et al, 1978) that are homologous to the individual domains of u-PA have been previously determined, the three-dimensional structure of u-PA may differ in key areas, since its biological functions and binding specificities are vastly different from the homologous proteins whose structures have been solved.…”

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confidence: 99%

Solution Structure of the Amino-Terminal Fragment of Urokinase-Type Plasminogen Activator

Hansen¹,

Petros²,

Meadows³

et al. 1994

Biochemistry

100

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The amino-terminal fragment (ATF) of urokinase-type plasminogen activator is a two domain protein which consists of a growth factor and a kringle domain. The 1H, 13C, and 15N chemical shifts of this protein have been assigned using heteronuclear two- and three-dimensional NMR experiments on selective and uniformly 15N- and 15N/13C-labeled protein isolated from mammalian cells that overexpress the protein. The chemical shift assignments were used to interpret the NOE data which resulted in a total of 1299 NOE restraints. The NOE restraints were used along with 27 phi angle restraints and 21 hydrogen-bonding restraints to produce 15 low energy structures. The individual domains in the structures are highly converged, but the two domains are structurally independent. The root mean square deviations (rmsd) between residues 11-46 in the growth factor domain and the mean atomic coordinates were 0.99 +/- 0.2 for backbone heavy atoms and 1.65 +/- 0.2 for all non-hydrogen atoms. For residues 55-130 in the kringle domain, the rmsd was 0.84 +/- 0.2 for backbone heavy atoms and 1.42 +/- 0.2 for all non-hydrogen atoms. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor and other homologous proteins were observed in the region which has been implicated in binding the urokinase receptor which may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor.

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The structure of α-chymotrypsin. I. The refinement of the heavy-atom isomorphous derivatives at 2.8 Å resolution

Cited by 40 publications

References 5 publications

Model for haptoglobin heavy chain based upon structural homology.

Model for haptoglobin heavy chain based upon structural homology.

Kringle‐kringle interactions in multimer kringle structures

Solution Structure of the Amino-Terminal Fragment of Urokinase-Type Plasminogen Activator

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