Crystallographic refinement of Japanese quail ovomucoid, a Kazal-type inhibitor, and model building studies of complexes with serine proteases

Papamokos, Evangelos; Weber, Ernst; Bode, Wolfram; Huber, Robert; Empie, Mark W.; Kato, Ikuo; Laskowski, M.

doi:10.1016/0022-2836(82)90212-1

Cited by 145 publications

(89 citation statements)

References 20 publications

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“…deviation of 0.037 nm. This value differs only slightly from the values derived for the four non-equivalent molecules of OMJPQ3 [3]. Therefore, the qualitative description of the OMJPQ3 structure, as given by these authors, remains valid also for the OMSVP3 molecule.…”

Section: Omsvp3 and Omjpq3mentioning

confidence: 51%

“…It is interesting to observe that the carbonyl groups of Glu-19 are almost congruent in both molecules and those of Thr-17 similarly oriented. As had been first proposed for the OMJPQ3 structure [3] and also suggested by its strong conservation in the Kazal inhibitor family [18]. Asn-33 acts as a spacer between the primary binding segment and the central parts of the molecule.…”

Section: Omsvp3 and Omtky3mentioning

confidence: 89%

“…It is, however, replaced by non-carboxylic amino acids in other Kazal inhibitors, which could not make such an intra-residue hydrogen bond (see e.g. [3]). In our free OMSVP3 molecule, the distance between Glu-19 0" and N is too long for a hydrogen bond.…”

Section: Omsvp3 and Omtky3mentioning

confidence: 99%

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The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3)

Bode

Epp

Huber

et al. 1985

European Journal of Biochemistry

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OMSVP3 and Oh4TKY3 (third domains of silver pheasant and turkey ovomucoid inhibitor) are Kazal-type serine proteinase inhbitors. They have been isomorphously crystallized in the monoclinic space group C2 with cell dimensions of a = 4.429 nm, b = 2.115 nm, c = 4.405 nm, /3 = 107". The asymmetric unit contains one molecule corresponding to an extremely low volume per unit molecular mass of 0.0017 nm3/Da. Data collection was only possible for the OMSVP3 crystals. Orientation and position of the OMSVP3 molecules in the monoclinic unit cells were determined using Patterson search methods and the known structure of the third domain of Japanese quail ovomucoid (OMJPQ3) [Papamokos, E., Weber, E., Bode, W., Huber, R., Empie, M. W., Kato, I. Ovomucoid inhibitors are major constitutents of avian egg white. Generally they consist of three tandem domains, each of which is a strong inhibitor of serine proteases and belongs to the family of Kazal inhibitors. The specificity of the ovomucoid inhibitors is mainly determined by the P1 residue. The nomenclature of Schechter and Berger [l] is used for the numbering of the substrate amino acid residues 'towards the NH2-terminal and the COOH-terminal directions from the scissile bond. The detailed specificity is also affected by single residue changes in positions other than P1. In an attempt to unravel the detailed algorithm for predicting inhibitory specificity from the amino acid sequence the Purdue group has sequenced a large number of avian ovomucoid domains and compared their inhibitory properties. It was found that only changes of residues in contact with the enzyme are important. Such exchanges may affect the packing of the inhibitory enzyme interface but they may also alter the mainchain conformation of the binding segment itself. Structural studies of related inhibitors are required to clarify this problem.The high-resolution crystal structures of three different representatives of the Kazal family have been determined and crystallographically refined : four independent molecules per asymmetric unit of the third domain of Japanese quail ovomucoid inhibitor (OMJPQ3) [2, 31, the third domain of turkey ovomucoid inhibitor (OMTKY3) complexed with the Abbreviations. OMSVP3, third domain of silver pheasant ovomucoid inhibitor; Oh4TKY3, third domain of turkey ovomucoid inhibitor; OMJPQ3, third domain of Japanese quail ovomucoid inhibitor; PSTI, porcine pancreatic trypsin inhibitor; SGPB, Streptomyces griseus protease B; r.m.s., root-mean-square; IFo\, IF& observed and computed structure amplitudes.Streptomyces griseus protease B [4,5], and the porcine pancreatic secretory trypsin inhibitor (PSTI) complexed with bovine trypsinogen [6]. The sequence of OMSVP3 differs at six positions from OMJPQ3. Three of these changes occur at P2(17), Pl(18) and Pl'(19) around the reactive site. The P3 to P2' residues run as follows: Cys-16, Thr-17, Met-18, Glu-19, Tyr-20. Thus, in contrast to OMJPQ3, which is a trypsin inhibitor because of a lysine residue at its PI position, the methionine of OMS...

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Section: Omsvp3 and Omjpq3mentioning

confidence: 51%

Section: Omsvp3 and Omtky3mentioning

confidence: 89%

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The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3)

Bode

Epp

Huber

et al. 1985

European Journal of Biochemistry

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121

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“…The ovomucoid domain consists of about 56 residues (Laskowski et al, 1987). The fold, as revealed by a 1.9-A crystal structure (PDB entry 20VO) begins with a 20-residue Reprint requests to: M. Levitt, Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford University School of Medicine,Stanford,California 94305; N-terminal loop region (Papamokos et al, 1982). This is followed by a 3-stranded antiparallel 0-sheet and a single a-helix, which pack together to form a hydrophobic core (Fig.…”

mentioning

confidence: 99%

“…A model of the ovomucoid-trypsin complex shows that main-chain hydrogen bonds are largely responsible for the stability of the binding interaction (Papamokos et al, 1982). Four copies of L7/L12 are found on the surface of the large subunit of prokaryote ribosomes (Gudkov et al, 1978b).…”

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confidence: 99%

Different protein sequences can give rise to highly similar folds through different stabilizing interactions

Laurents

Subbiah²,

Levitt

1994

Protein Science

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We report an interesting case of structural similarity between 2 small, nonhomologous proteins, the third domain of ovomucoid (ovomucoid) and the C-terminal fragment of ribosomal L7/L12 protein (CTF). The region of similarity consists of a 3-stranded 0-sheet and an a-helix. This region is highly similar; the corresponding elements of secondary structure share a common topology, and the RMS difference for "equivalent" C a atoms is 1.6 A.Surprisingly, this common structure arises from completely different sequences. For the common core, the sequence identity is less than 3%, and there is neither significant sequence similarity nor similarity in the position or orientation of conserved hydrophobic residues. This superposition raises the question of how 2 entirely different sequences can produce an identical structure. Analyzing this common region in ovomucoid revealed that it is stabilized by disulfide bonds. In contrast, the corresponding structure in CTF is stabilized in the a-helix by a composition of residues with high helix-forming propensities. This result suggests that different sequences and different stabilizing interactions can produce an identical structure.Keywords: CTF; evolution; ovomucoid; protein design; protein folding; sequence; structure; structure superpositionThe tremendous growth of the number of solved protein structures has created a need for new automatic methods for structural comparison (Bowie et al., 1991). Such methods are useful because they allow the detection of homology in the many cases where distantly related proteins have lost sequence similarity but still retain a common structure (Rossmann et al., 1974;Matthews et al., 1981). Protein structure comparison can also offer insights into the interrelationships between sequence, structure, and function. To fill this need, we have developed a rapid, quantitative method for comparing pairs of protein structures. In the course of examining the results of all possible pairwise comparisons of protein structures in the Protein Data Bank (PDB), we were first startled to find structural similarity between proteins of the repressor and globin families (Subbiah et al., 1993). Here, we report a second case of notable structural similarity, between the third domain of ovomucoid (ovomucoid) and the C-terminal fragment of ribosomal L7/L12 protein (CTF).Ovomucoid and CTF are small proteins belonging to the a+P structure class. The ovomucoid domain consists of about 56 residues (Laskowski et al., 1987). The fold, as revealed by a 1.9-A crystal structure (PDB entry 20VO) begins with a 20-residue

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Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

1999

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A new dataset of 396 protein domains is developed and used to evaluate the performance of the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR. The maximum theoretical Q 3 accuracy for combination of these methods is shown to be 78%. A simple consensus prediction on the 396 domains, with automatically generated multiple sequence alignments gives an average Q 3 prediction accuracy of 72.9%. This is a 1% improvement over PHD, which was the best single method evaluated. Segment Overlap Accuracy (SOV) is 75.4% for the consensus method on the 396-protein set. The secondary structure definition method DSSP defines 8 states, but these are reduced by most authors to 3 for prediction. Application of the different published 8-to 3-state reduction methods shows variation of over 3% on apparent prediction accuracy. This suggests that care should be taken to compare methods by the same reduction method. Two new sequence datasets (CB513 and CB251) are derived which are suitable for cross-validation of secondary structure prediction methods without artifacts due to internal homology. A fully automatic World Wide Web service that predicts protein secondary structure by a combination of methods is available via http://barton.ebi.ac.uk/. Proteins 1999;34:508-519.

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Crystallographic refinement of Japanese quail ovomucoid, a Kazal-type inhibitor, and model building studies of complexes with serine proteases

Cited by 145 publications

References 20 publications

The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3)

The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3)

Different protein sequences can give rise to highly similar folds through different stabilizing interactions

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

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