spacer
spacer

PDBsum entry 1ova

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Serpin PDB id
1ova

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
386 a.a. *
Ligands
NAG ×4
Metals
_CA
Waters ×678
* Residue conservation analysis
PDB id:
1ova
Name: Serpin
Title: Crystal structure of uncleaved ovalbumin at 1.95 angstroms resolution
Structure: Ovalbumin. Chain: a. Engineered: yes. Ovalbumin. Chain: b. Engineered: yes. Ovalbumin. Chain: c, d. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031
Biol. unit: Dimer (from PQS)
Resolution:
1.95Å     R-factor:   0.169    
Authors: P.E.Stein,A.G.W.Leslie
Key ref: P.E.Stein et al. (1991). Crystal structure of uncleaved ovalbumin at 1.95 A resolution. J Mol Biol, 221, 941-959. PubMed id: 1942038
Date:
26-Nov-90     Release date:   15-Apr-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01012  (OVAL_CHICK) -  Ovalbumin from Gallus gallus
Seq:
Struc:
386 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
J Mol Biol 221:941-959 (1991)
PubMed id: 1942038  
 
 
Crystal structure of uncleaved ovalbumin at 1.95 A resolution.
P.E.Stein, A.G.Leslie, J.T.Finch, R.W.Carrell.
 
  ABSTRACT  
 
Ovalbumin, the major protein in avian egg-white, is a non-inhibitory member of the serine protease inhibitor (serpin) superfamily. The crystal structure of uncleaved, hen ovalbumin was solved by the molecular replacement method using the structure of plakalbumin, a proteolytically cleaved form of ovalbumin, as a starting model. The final refined model, including four ovalbumin molecules, 678 water molecules and a single metal ion, has a crystallographic R-factor of 17.4% for all reflections between 6.0 and 1.95 A resolution. The root-mean-square deviation from ideal values in bond lengths is 0.02 A and in bond angles is 2.9 degrees. This is the first crystal structure of a member of the serpin family in an uncleaved form. Surprisingly, the peptide that is homologous to the reactive centre of inhibitory serpins adopts an alpha-helical conformation. The implications for the mechanism of inhibition of the inhibitory members of the family is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20703954 A.Naeem, T.A.Khan, M.Muzaffar, S.Ahmad, and M.Saleemuddin (2011).
A partially folded state of ovalbumin at low pH tends to aggregate.
  Cell Biochem Biophys, 59, 29-38.  
21264428 F.Berti, S.Bincoletto, I.Donati, G.Fontanive, M.Fregonese, and F.Benedetti (2011).
Albumin-directed stereoselective reduction of 1,3-diketones and β-hydroxyketones to anti diols.
  Org Biomol Chem, 9, 1987-1999.  
21389617 T.Ishimaru, K.Ito, M.Tanaka, S.Tanaka, and N.Matsudomi (2011).
The role of the disulfide bridge in the stability and structural integrity of ovalbumin evaluated by site-directed mutagenesis.
  Biosci Biotechnol Biochem, 75, 544-549.  
20564677 N.Takahashi, M.Maeda, M.Yamasaki, and B.Mikami (2010).
Protein-engineering study of contribution of conceivable D-serine residues to the thermostabilization of ovalbumin under alkaline conditions.
  Chem Biodivers, 7, 1634-1643.  
20512973 T.Ishimaru, K.Ito, M.Tanaka, and N.Matsudomi (2010).
Thermostabilization of ovalbumin by alkaline treatment: Examination of the possible roles of D-serine residues.
  Protein Sci, 19, 1205-1212.  
  18713974 J.M.Weaver, C.A.Lazarski, K.A.Richards, F.A.Chaves, S.A.Jenks, P.R.Menges, and A.J.Sant (2008).
Immunodominance of CD4 T cells to foreign antigens is peptide intrinsic and independent of molecular context: implications for vaccine design.
  J Immunol, 181, 3039-3048.  
18390904 M.Onda, K.Nakatani, S.Takehara, M.Nishiyama, N.Takahashi, and M.Hirose (2008).
Cleaved serpin refolds into the relaxed state via a stressed conformer.
  J Biol Chem, 283, 17568-17578.  
18838817 T.Matsubara, N.Aoki, T.Honjoh, K.Mizumachi, J.Kurisaki, T.Okajima, D.Nadano, and T.Matsuda (2008).
Absorption, migration and kinetics in peripheral blood of orally administered ovalbumin in a mouse model.
  Biosci Biotechnol Biochem, 72, 2555-2565.  
17766383 A.C.Dumetz, A.M.Snellinger-O'brien, E.W.Kaler, and A.M.Lenhoff (2007).
Patterns of protein protein interactions in salt solutions and implications for protein crystallization.
  Protein Sci, 16, 1867-1877.  
17154314 J.de Groot, H.A.Kosters, and H.H.de Jongh (2007).
Deglycosylation of ovalbumin prohibits formation of a heat-stable conformer.
  Biotechnol Bioeng, 97, 735-741.  
17644521 M.A.Klieber, C.Underhill, G.L.Hammond, and Y.A.Muller (2007).
Corticosteroid-binding globulin, a structural basis for steroid transport and proteinase-triggered release.
  J Biol Chem, 282, 29594-29603.
PDB codes: 2v6d 2v95
16617426 H.Deng, G.Chen, W.Yang, and J.J.Yang (2006).
Predicting calcium-binding sites in proteins - a graph theory and geometry approach.
  Proteins, 64, 34-42.  
16689933 M.Oda, S.Uchiyama, C.V.Robinson, K.Fukui, Y.Kobayashi, and T.Azuma (2006).
Regional and segmental flexibility of antibodies in interaction with antigens of different size.
  FEBS J, 273, 1476-1487.  
16421915 M.V.Cañamares, P.Sevilla, S.Sanchez-Cortes, and J.V.Garcia-Ramos (2006).
Surface-enhanced Raman scattering study of the interaction of red dye alizarin with ovalbumin.
  Biopolymers, 82, 405-409.  
15659378 E.V.Kudryashova, A.J.Visser, and H.H.De Jongh (2005).
Reversible self-association of ovalbumin at air-water interfaces and the consequences for the exerted surface pressure.
  Protein Sci, 14, 483-493.  
15964983 J.H.Lee, J.M.Choi, C.Lee, K.J.Yi, and Y.Cho (2005).
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
  Proc Natl Acad Sci U S A, 102, 9144-9149.
PDB codes: 1x3w 1x3z
15618616 F.Tani, N.Shirai, Y.Nakanishi, K.Yasumoto, and N.Kitabatake (2004).
Role of the carbohydrate chain and two phosphate moieties in the heat-induced aggregation of hen ovalbumin.
  Biosci Biotechnol Biochem, 68, 2466-2476.  
12930828 E.M.Springhetti, N.E.Istomina, J.C.Whisstock, T.Nikitina, C.L.Woodcock, and S.A.Grigoryev (2003).
Role of the M-loop and reactive center loop domains in the folding and bridging of nucleosome arrays by MENT.
  J Biol Chem, 278, 43384-43393.  
12649292 E.Marszal, D.Danino, and A.Shrake (2003).
A novel mode of polymerization of alpha1-proteinase inhibitor.
  J Biol Chem, 278, 19611-19618.  
12834280 F.Tani, N.Shirai, Y.Nakanishi, and N.Kitabatake (2003).
Analysis of molecular interactions in heat-induced aggregation of a non-inhibitory serpin ovalbumin using a molecular chaperone.
  Biosci Biotechnol Biochem, 67, 1030-1038.  
12910544 H.A.Kosters, K.Broersen, J.de Groot, J.W.Simons, P.Wierenga, and H.H.de Jongh (2003).
Chemical processing as a tool to generate ovalbumin variants with changed stability.
  Biotechnol Bioeng, 84, 61-70.  
12711610 M.Onda, and M.Hirose (2003).
Refolding mechanism of ovalbumin: investigation by using a starting urea-denatured disulfide isomer with mispaired CYS367-CYS382.
  J Biol Chem, 278, 23600-23609.  
12840013 M.Yamasaki, N.Takahashi, and M.Hirose (2003).
Crystal structure of S-ovalbumin as a non-loop-inserted thermostabilized serpin form.
  J Biol Chem, 278, 35524-35530.
PDB code: 1uhg
14615091 R.J.Whelan, and R.N.Zare (2003).
Single-cell immunosensors for protein detection.
  Biosens Bioelectron, 19, 331-336.  
14529288 S.Taneva, J.E.Johnson, and R.B.Cornell (2003).
Lipid-induced conformational switch in the membrane binding domain of CTP:phosphocholine cytidylyltransferase: a circular dichroism study.
  Biochemistry, 42, 11768-11776.  
12729000 Y.Arii, N.Takahashi, and M.Hirose (2003).
Periplasmic secretion of native ovalbumin without signal cleavage in Escherichia coli.
  Biosci Biotechnol Biochem, 67, 368-371.  
11821386 J.A.Irving, S.S.Shushanov, R.N.Pike, E.Y.Popova, D.Brömme, T.H.Coetzer, S.P.Bottomley, I.A.Boulynko, S.A.Grigoryev, and J.C.Whisstock (2002).
Inhibitory activity of a heterochromatin-associated serpin (MENT) against papain-like cysteine proteinases affects chromatin structure and blocks cell proliferation.
  J Biol Chem, 277, 13192-13201.  
12209447 K.Murayama, and Y.Ozaki (2002).
Two-dimensional near-IR correlation spectroscopy study of molten globule-like state of ovalbumin in acidic pH region: simultaneous changes in hydration and secondary structure.
  Biopolymers, 67, 394-405.  
  11890617 E.Lund, I.B.Rasmussen, K.H.Western, J.K.Eidem, I.Sandlie, and B.Bogen (2001).
"Troy-bodies": recombinant antibodies that target T cell epitopes to antigen presenting cells.
  Int Rev Immunol, 20, 647-673.  
11135188 H.Y.Hu, Q.Li, H.C.Cheng, and H.N.Du (2001).
beta-sheet structure formation of proteins in solid state as revealed by circular dichroism spectroscopy.
  Biopolymers, 62, 15-21.  
11517321 I.B.Rasmussen, E.Lunde, T.E.Michaelsen, B.Bogen, and I.Sandlie (2001).
The principle of delivery of T cell epitopes to antigen-presenting cells applied to peptides from influenza virus, ovalbumin, and hen egg lysozyme: implications for peptide vaccination.
  Proc Natl Acad Sci U S A, 98, 10296-10301.  
11546761 L.Jankova, S.J.Harrop, D.N.Saunders, J.L.Andrews, K.C.Bertram, A.R.Gould, M.S.Baker, and P.M.Curmi (2001).
Crystal structure of the complex of plasminogen activator inhibitor 2 with a peptide mimicking the reactive center loop.
  J Biol Chem, 276, 43374-43382.
PDB code: 1jrr
11536359 O.Schueler-Furman, Y.Altuvia, and H.Margalit (2001).
Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.
  Proteins, 45, 47-54.  
11461047 S.Henriot, J.P.Lepoitrevin, and E.Trifilieff (2001).
Haptenization of ovalbumin with the skin sensitizer methyl octanesulfonate: characterization of the methylated OVA323-339 T-cell epitope at His331.
  J Pept Sci, 7, 331-337.  
11826952 Y.Sun, and S.Hayakawa (2001).
Sequential comparison of peptides containing half-cystine residues from ovalbumins of six avian species.
  Biosci Biotechnol Biochem, 65, 2589-2596.  
10744333 D.Bailey, D.V.Renouf, D.G.Large, C.D.Warren, and E.F.Hounsell (2000).
Conformational studies of the glycopeptide Ac-Tyr-[Man5GlcNAc-beta-(1-->4)GlcNAc-beta-(1-->Ndelta)]-Asn-Leu-Thr-Se r-OBz and the constituent peptide and oligosaccharide.
  Carbohydr Res, 324, 242-254.  
10885394 K.Monkos (2000).
Viscosity analysis of the temperature dependence of the solution conformation of ovalbumin.
  Biophys Chem, 85, 7.  
10520251 C.J.Beverung, C.J.Radke, and H.W.Blanch (1999).
Protein adsorption at the oil/water interface: characterization of adsorption kinetics by dynamic interfacial tension measurements.
  Biophys Chem, 81, 59-80.  
10478455 E.Tatsumi, D.Yoshimatsu, and M.Hirose (1999).
Conformational state of disulfide-reduced ovalbumin at acidic pH.
  Biosci Biotechnol Biochem, 63, 1285-1290.  
10026180 S.A.Grigoryev, J.Bednar, and C.L.Woodcock (1999).
MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new serpin family member.
  J Biol Chem, 274, 5626-5636.  
10233060 S.E.Harding, J.C.Horton, S.Jones, J.M.Thornton, and D.J.Winzor (1999).
COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.
  Biophys J, 76, 2432-2438.  
10368272 S.J.Harrop, L.Jankova, M.Coles, D.Jardine, J.S.Whittaker, A.R.Gould, A.Meister, G.C.King, B.C.Mabbutt, and P.M.Curmi (1999).
The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: implications for serpin function.
  Structure, 7, 43-54.
PDB code: 1by7
10514431 T.Liu, P.A.Pemberton, and A.D.Robertson (1999).
Three-state unfolding and self-association of maspin, a tumor-suppressing serpin.
  J Biol Chem, 274, 29628-29632.  
10501000 Y.Arii, N.Takahashi, E.Tatsumi, and M.Hirose (1999).
Structural properties of recombinant ovalbumin and its transformation into a thermostabilized form by alkaline treatment.
  Biosci Biotechnol Biochem, 63, 1392-1399.  
9468513 C.E.Chaillan-Huntington, and P.A.Patston (1998).
Influence of the P5 residue on alpha1-proteinase inhibitor mechanism.
  J Biol Chem, 273, 4569-4573.  
9692954 E.Alberdi, C.C.Hyde, and S.P.Becerra (1998).
Pigment epithelium-derived factor (PEDF) binds to glycosaminoglycans: analysis of the binding site.
  Biochemistry, 37, 10643-10652.  
9724549 E.Tatsumi, D.Yoshimatsu, and M.Hirose (1998).
Conformational state of ovalbumin at acidic pH as evaluated by a novel approach utilizing intrachain sulfhydryl-mixed disulfide exchange reactions.
  Biochemistry, 37, 12351-12359.  
9538691 J.Whisstock, R.Skinner, and A.M.Lesk (1998).
An atlas of serpin conformations.
  Trends Biochem Sci, 23, 63-67.  
9236002 C.E.Chaillan-Huntington, P.G.Gettins, J.A.Huntington, and P.A.Patston (1997).
The P6-P2 region of serpins is critical for proteinase inhibition and complex stability.
  Biochemistry, 36, 9562-9570.  
9235938 E.Ersdal-Badju, A.Lu, Y.Zuo, V.Picard, and S.C.Bock (1997).
Identification of the antithrombin III heparin binding site.
  J Biol Chem, 272, 19393-19400.  
  9232650 F.Tani, N.Shirai, T.Onishi, F.Venelle, K.Yasumoto, and E.Doi (1997).
Temperature control for kinetic refolding of heat-denatured ovalbumin.
  Protein Sci, 6, 1491-1502.  
  9348117 H.L.Fitton, R.N.Pike, R.W.Carrell, and W.S.Chang (1997).
Mechanisms of antithrombin polymerisation and heparin activation probed by the insertion of synthetic reactive loop peptides.
  Biol Chem, 378, 1059-1063.  
9154925 J.A.Huntington, B.Fan, K.E.Karlsson, J.Deinum, D.A.Lawrence, and P.G.Gettins (1997).
Serpin conformational change in ovalbumin. Enhanced reactive center loop insertion through hinge region mutations.
  Biochemistry, 36, 5432-5440.  
  8670857 B.Holst, A.W.Bruun, M.C.Kielland-Brandt, and J.R.Winther (1996).
Competition between folding and glycosylation in the endoplasmic reticulum.
  EMBO J, 15, 3538-3546.  
  8732755 B.O.Villoutreix, H.Lilja, K.Pettersson, T.Lövgren, and O.Teleman (1996).
Structural investigation of the alpha-1-antichymotrypsin: prostate-specific antigen complex by comparative model building.
  Protein Sci, 5, 836-851.  
8813337 D.A.Lane, G.Kunz, R.J.Olds, and S.L.Thein (1996).
Molecular genetics of antithrombin deficiency.
  Blood Rev, 10, 59-74.  
  8976566 E.Stratikos, E.Alberdi, P.G.Gettins, and S.P.Becerra (1996).
Recombinant human pigment epithelium-derived factor (PEDF): characterization of PEDF overexpressed and secreted by eukaryotic cells.
  Protein Sci, 5, 2575-2582.  
8679610 J.A.Huntington, S.T.Olson, B.Fan, and P.G.Gettins (1996).
Mechanism of heparin activation of antithrombin. Evidence for reactive center loop preinsertion with expulsion upon heparin binding.
  Biochemistry, 35, 8495-8503.  
8652792 V.Pavone, G.Gaeta, A.Lombardi, F.Nastri, O.Maglio, C.Isernia, and M.Saviano (1996).
Discovering protein secondary structures: classification and description of isolated alpha-turns.
  Biopolymers, 38, 705-721.  
7622502 D.A.Lomas, P.R.Elliott, S.K.Sidhar, R.C.Foreman, J.T.Finch, D.W.Cox, J.C.Whisstock, and R.W.Carrell (1995).
alpha 1-Antitrypsin Mmalton (Phe52-deleted) forms loop-sheet polymers in vivo. Evidence for the C sheet mechanism of polymerization.
  J Biol Chem, 270, 16864-16870.  
7890640 D.A.Lomas, P.R.Elliott, W.S.Chang, M.R.Wardell, and R.W.Carrell (1995).
Preparation and characterization of latent alpha 1-antitrypsin.
  J Biol Chem, 270, 5282-5288.  
7664104 H.M.Tucker, J.Mottonen, E.J.Goldsmith, and R.D.Gerard (1995).
Engineering of plasminogen activator inhibitor-1 to reduce the rate of latency transition.
  Nat Struct Biol, 2, 442-445.
PDB code: 1c5g
  7613461 J.A.Huntington, P.A.Patston, and P.G.Gettins (1995).
S-ovalbumin, an ovalbumin conformer with properties analogous to those of loop-inserted serpins.
  Protein Sci, 4, 613-621.  
7722450 K.A.Barnes, and R.N.Mitchell (1995).
Detection of functional class II-associated antigen: role of a low density endosomal compartment in antigen processing.
  J Exp Med, 181, 1715-1727.  
7592909 M.Riewald, and R.R.Schleef (1995).
Molecular cloning of bomapin (protease inhibitor 10), a novel human serpin that is expressed specifically in the bone marrow.
  J Biol Chem, 270, 26754-26757.  
18623492 R.A.Judge, M.R.Johns, and E.T.White (1995).
Protein purification by bulk crystallization: The recovery of ovalbumin.
  Biotechnol Bioeng, 48, 316-323.  
  17607884 R.Carrell, R.Skinner, M.Warden, and J.Whisstock (1995).
Antithrombin and heparin.
  Mol Med Today, 1, 226-231.  
7721731 S.K.Sidhar, D.A.Lomas, R.W.Carrell, and R.C.Foreman (1995).
Mutations which impede loop/sheet polymerization enhance the secretion of human alpha 1-antitrypsin deficiency variants.
  J Biol Chem, 270, 8393-8396.  
7656054 A.Wei, H.Rubin, B.S.Cooperman, and D.W.Christianson (1994).
Crystal structure of an uncleaved serpin reveals the conformation of an inhibitory reactive loop.
  Nat Struct Biol, 1, 251-258.  
8205009 D.J.Perry (1994).
Antithrombin and its inherited deficiencies.
  Blood Rev, 8, 37-55.  
7656006 H.A.Schreuder, B.de Boer, R.Dijkema, J.Mulders, H.J.Theunissen, P.D.Grootenhuis, and W.G.Hol (1994).
The intact and cleaved human antithrombin III complex as a model for serpin-proteinase interactions.
  Nat Struct Biol, 1, 48-54.
PDB code: 1ath
8064333 I.Callebaut, A.Tasso, R.Brasseur, A.Burny, D.Portetelle, and J.P.Mornon (1994).
Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: do prions possess a fusion peptide?
  J Comput Aided Mol Des, 8, 175-191.  
8017761 P.A.Patston, P.G.Gettins, and M.Schapira (1994).
The mechanism by which serpins inhibit thrombin and other serine proteinases.
  Ann N Y Acad Sci, 714, 13-20.  
7947262 R.J.Olds, D.A.Lane, and S.L.Thein (1994).
The molecular genetics of antithrombin deficiency.
  Br J Haematol, 87, 221-226.  
8087553 R.W.Carrell, P.E.Stein, G.Fermi, and M.R.Wardell (1994).
Biological implications of a 3 A structure of dimeric antithrombin.
  Structure, 2, 257-270.
PDB code: 1ant
7922041 Y.Harpaz, M.Gerstein, and C.Chothia (1994).
Volume changes on protein folding.
  Structure, 2, 641-649.  
1469094 D.A.Lane, R.J.Olds, J.Conard, M.Boisclair, S.C.Bock, M.Hultin, U.Abildgaard, H.Ireland, E.Thompson, and G.Sas (1992).
Pleiotropic effects of antithrombin strand 1C substitution mutations.
  J Clin Invest, 90, 2422-2433.  
1368442 D.C.Crowther, D.L.Evans, and R.W.Carrell (1992).
Serpins: implications of a mobile reactive centre.
  Curr Opin Biotechnol, 3, 399-407.  
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.

 

spacer

spacer