spacer
spacer

PDBsum entry 3ovo

Go to PDB code: 
protein links
Proteinase inhibitor (kazal) PDB id
3ovo
Jmol
Contents
Protein chain
56 a.a. *
Waters ×34
* Residue conservation analysis
PDB id:
3ovo
Name: Proteinase inhibitor (kazal)
Title: Refined x-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (omsvp3(asterisk)) and from japanese quail (omjpq3(asterisk))
Structure: Ovomucoid third domain cleaved rdi. Chain: a. Engineered: yes
Source: Coturnix japonica. Japanese quail. Organism_taxid: 93934
Resolution:
1.55Å     R-factor:   0.192    
Authors: D.Musil,W.Bode
Key ref: D.Musil et al. (1991). Refined X-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (OMSVP3*) and from Japanese quail (OMJPQ3*). J Mol Biol, 220, 739-755. PubMed id: 1870129
Date:
13-May-91     Release date:   15-Jan-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01003  (IOVO_COTJA) -  Ovomucoid
Seq:
Struc:
186 a.a.
56 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     serine-type endopeptidase inhibitor activity     1 term  

 

 
J Mol Biol 220:739-755 (1991)
PubMed id: 1870129  
 
 
Refined X-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (OMSVP3*) and from Japanese quail (OMJPQ3*).
D.Musil, W.Bode, R.Huber, M.Laskowski, T.Y.Lin, W.Ardelt.
 
  ABSTRACT  
 
Tetragonal and triclinic crystals of two ovomucoid inhibitor third domains from silver pheasant and Japanese quail, modified at their reactive site bonds Met18-Glu19 (OMSVP3*) and Lys18-Asp19 (OMJPQ3*), respectively, were obtained. Their molecular and crystal structures were solved using X-ray data to 2.5 A and 1.55 A by means of Patterson search methods using truncated models of the intact (virgin) inhibitors as search models. Both structures were crystallographically refined to R-values of 0.185 and 0.192, respectively, applying an energy restraint reciprocal space refinement procedure. Both modified inhibitors show large deviations from the intact derivatives only in the proteinase binding loops (Pro14 to Arg21) and in the amino-terminal segments (Leu1 to Val6). In the modified inhibitors the residues immediately adjacent to the cleavage site (in particular P2, P1, P1') are mobile and able to adapt to varying crystal environments. The charged end-groups, i.e. Met18 COO- and Glu19 NH3+ in OMSVP3*, and Lys18 COO- and Asp19 NH3+ in OMJPQ3*, do not form ion pairs with one another. The hydrogen bond connecting the side-chains of Thr17 and Glu19 (i.e. residues on either side of the scissile peptide bond) in OMSVP3 is broken in the modified form, and the hydrogen-bond interactions observed in the intact molecules between the Asn33 side-chain and the carbonyl groups of loop residues P2 and P1' are absent or weak in the modified inhibitors. The reactive site cleavage, however, has little effect on specific interactions within the protein scaffold such as the side-chain hydrogen bond between Asp27 and Tyr31 or the side-chain stacking of Tyr20 and Pro22. The conformational differences in the amino-terminal segment Leu1 to Val6 are explained by their ability to move freely, either to associate with segments of symmetry-related molecules under formation of a four-stranded beta-barrel (OMSVP3* and OMJPQ3) or to bind to surrounding molecules. Together with the results given in the accompanying paper, these findings probably explain why Khyd of small protein inhibitors of serine proteinases is generally found to be so small.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
15775973 J.Otlewski, F.Jelen, M.Zakrzewska, and A.Oleksy (2005).
The many faces of protease-protein inhibitor interaction.
  EMBO J, 24, 1303-1310.  
11910035 O.Buczek, D.Krowarsch, and J.Otlewski (2002).
Thermodynamics of single peptide bond cleavage in bovine pancreatic trypsin inhibitor (BPTI).
  Protein Sci, 11, 924-932.  
9689072 A.M.Deacon, C.M.Weeks, R.Miller, and S.E.Ealick (1998).
The Shake-and-Bake structure determination of triclinic lysozyme.
  Proc Natl Acad Sci U S A, 95, 9284-9289.  
  9514268 J.Liu, Y.Gong, O.Prakash, L.Wen, I.Lee, J.K.Huang, and R.Krishnamoorthi (1998).
NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family.
  Protein Sci, 7, 132-141.  
  8535235 K.Huang, W.Lu, S.Anderson, M.Laskowski, and M.N.James (1995).
Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.
  Protein Sci, 4, 1985-1997.
PDB codes: 1sgp 1sgq 1sgr
8569452 P.Ascenzi, G.Amiconi, W.Bode, M.Bolognesi, M.Coletta, and E.Menegatti (1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
  Mol Aspects Med, 16, 215-313.  
8595135 R.A.Engh, R.Huber, W.Bode, and A.J.Schulze (1995).
Divining the serpin inhibition mechanism: a suicide substrate 'springe'?
  Trends Biotechnol, 13, 503-510.  
8081735 C.Chothia, and A.G.Murzin (1993).
New folds for all-beta proteins.
  Structure, 1, 217-222.  
8427637 P.C.Sil, T.K.Chaudhuri, and N.K.Sinha (1993).
Basic trypsin-subtilisin inhibitor from marine turtle egg white: hydrodynamic and inhibitory properties.
  J Protein Chem, 12, 71-78.  
1541261 W.Bode, and R.Huber (1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
  Eur J Biochem, 204, 433-451.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.