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PDBsum entry 1utg

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protein links
Steroid binding PDB id
1utg
Jmol
Contents
Protein chain
70 a.a. *
Waters ×83
* Residue conservation analysis
PDB id:
1utg
Name: Steroid binding
Title: Refinement of the c2221 crystal form of oxidized uteroglobin angstroms resolution
Structure: Uteroglobin. Chain: a. Engineered: yes
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986
Biol. unit: Dimer (from PQS)
Resolution:
1.34Å     R-factor:   0.230    
Authors: I.Morize,E.Surcouf,M.C.Vaney,M.Buehner,J.P.Mornon
Key ref: I.Morize et al. (1987). Refinement of the C222(1) crystal form of oxidized uteroglobin at 1.34 A resolution. J Mol Biol, 194, 725-739. PubMed id: 3656405
Date:
03-Apr-89     Release date:   15-Oct-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02779  (UTER_RABIT) -  Uteroglobin
Seq:
Struc:
91 a.a.
70 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     negative regulation of catalytic activity   9 terms 
  Biochemical function     lipid binding     3 terms  

 

 
J Mol Biol 194:725-739 (1987)
PubMed id: 3656405  
 
 
Refinement of the C222(1) crystal form of oxidized uteroglobin at 1.34 A resolution.
I.Morize, E.Surcouf, M.C.Vaney, Y.Epelboin, M.Buehner, F.Fridlansky, E.Milgrom, J.P.Mornon.
 
  ABSTRACT  
 
The structure of uteroglobin, a progesterone binding protein from rabbit uterine fluid, was determined and refined at 1.34 A resolution to a conventional R-factor of 0.229. The accuracy of the co-ordinates is estimated to be 0.15 A. The isotropic temperature factor of individual atoms was refined and its average value is 11.9 A2 for the 548 non-hydrogen atoms of the protein monomer. A total of 83 water molecules was located in difference electron density maps and refined, first using a constant occupancy factor of 1 and then variable occupancy, the final (Q) being 0.63. The mean temperature factor of the water oxygen atoms is 26.4 A2. Uteroglobin is a dimer and its secondary structure consists of four alpha-helices per monomer that align in an anti-parallel fashion. There is one beta-turn between helix 2 and helix 3 (Lys26 to Glu29); 76% of the residues are part of the alpha-helices. In the core of the dimeric protein molecule, between the two monomers that are held together by two disulfide bridges, we have observed a closed cavity. Its length is 15.6 A and its width is 9 A; 14 water molecules could be positioned inside. In the "bottom" part of the protein, near the C terminus, we have observed a smaller cavity, occupied by two water molecules. The calculation of the molecular surface revealed four surface pockets whose possible functional implications are discussed below.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19479996 E.Balza, F.Sassi, E.Ventura, A.Parodi, S.Fossati, W.Blalock, B.Carnemolla, P.Castellani, L.Zardi, and L.Borsi (2009).
A novel human fibronectin cryptic sequence unmasked by the insertion of the angiogenesis-associated extra type III domain B.
  Int J Cancer, 125, 751-758.  
19632988 E.Ventura, F.Sassi, S.Fossati, A.Parodi, W.Blalock, E.Balza, P.Castellani, L.Borsi, B.Carnemolla, and L.Zardi (2009).
Use of uteroglobin for the engineering of polyvalent, polyspecific fusion proteins.
  J Biol Chem, 284, 26646-26654.  
16849226 V.Cutello, G.Narzisi, and G.Nicosia (2006).
A multi-objective evolutionary approach to the protein structure prediction problem.
  J R Soc Interface, 3, 139-151.  
  16511079 V.von der Decken, H.Delbrück, A.Herrler, H.M.Beier, R.Fischer, and K.M.Hoffmann (2005).
Recombinant bovine uteroglobin at 1.6 A resolution: a preliminary X-ray crystallographic analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 499-502.  
12851385 L.Kaiser, H.Grönlund, T.Sandalova, H.G.Ljunggren, M.van Hage-Hamsten, A.Achour, and G.Schneider (2003).
The crystal structure of the major cat allergen Fel d 1, a member of the secretoglobin family.
  J Biol Chem, 278, 37730-37735.
PDB code: 1puo
14579361 R.P.Bahadur, P.Chakrabarti, F.Rodier, and J.Janin (2003).
Dissecting subunit interfaces in homodimeric proteins.
  Proteins, 53, 708-719.  
12022875 D.Carter, J.F.Douglass, C.D.Cornellison, M.W.Retter, J.C.Johnson, A.A.Bennington, T.P.Fleming, S.G.Reed, R.L.Houghton, D.L.Diamond, and T.S.Vedvick (2002).
Purification and characterization of the mammaglobin/lipophilin B complex, a promising diagnostic marker for breast cancer.
  Biochemistry, 41, 6714-6722.  
10024022 V.Prasanna, B.Gopal, M.R.Murthy, D.V.Santi, and P.Balaram (1999).
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase.
  Proteins, 34, 356-368.  
9712916 G.C.Kundu, A.K.Mandal, Z.Zhang, G.Mantile-Selvaggi, and A.B.Mukherjee (1998).
Uteroglobin (UG) suppresses extracellular matrix invasion by normal and cancer cells that express the high affinity UG-binding proteins.
  J Biol Chem, 273, 22819-22824.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9022046 Z.Zhang, D.B.Zimonjic, N.C.Popescu, N.Wang, D.S.Gerhard, E.M.Stone, N.C.Arbour, H.G.De Vries, H.Scheffer, J.Gerritsen, J.M.Colle'e, L.P.Ten Kate, and A.B.Mukherjee (1997).
Human uteroglobin gene: structure, subchromosomal localization, and polymorphism.
  DNA Cell Biol, 16, 73-83.  
9162944 L.Zhang, and J.Hermans (1996).
Hydrophilicity of cavities in proteins.
  Proteins, 24, 433-438.  
  8732757 X.de la Cruz, and B.Lee (1996).
The structural homology between uteroglobin and the pore-forming domain of colicin A suggests a possible mechanism of action for uteroglobin.
  Protein Sci, 5, 857-861.  
7615804 A.Peri, N.H.Dubin, R.Dhanireddy, and A.B.Mukherjee (1995).
Uteroglobin gene expression in the rabbit uterus throughout gestation and in the fetal lung. Relationship between uteroglobin and eicosanoid levels in the developing fetal lung.
  J Clin Invest, 96, 343-353.  
7583659 T.C.Umland, and M.Sax (1995).
Twixt form and function.
  Nat Struct Biol, 2, 919-922.  
7846028 J.H.Matthews, N.Pattabiraman, K.B.Ward, G.Mantile, L.Miele, and A.B.Mukherjee (1994).
Crystallization and characterization of the recombinant human Clara cell 10-kDa protein.
  Proteins, 20, 191-196.  
8159715 M.J.Bennett, S.Choe, and D.Eisenberg (1994).
Domain swapping: entangling alliances between proteins.
  Proc Natl Acad Sci U S A, 91, 3127-3131.  
8025221 S.Improta, A.Pastore, S.Mammi, and E.Peggion (1994).
Conformation and molecular dynamics calculations on uteroglobin fragment 18-47.
  Biopolymers, 34, 773-782.  
7922041 Y.Harpaz, M.Gerstein, and C.Chothia (1994).
Volume changes on protein folding.
  Structure, 2, 641-649.  
  8003958 Z.S.Hendsch, and B.Tidor (1994).
Do salt bridges stabilize proteins? A continuum electrostatic analysis.
  Protein Sci, 3, 211-226.  
8326954 C.Slingsby, O.A.Bateman, and A.Simpson (1993).
Motifs involved in protein-protein interactions.
  Mol Biol Rep, 17, 185-195.  
8268412 M.Tessari, M.T.Foffani, S.Mammi, and E.Peggion (1993).
Conformation and interactions of uteroglobin fragments 4-14 and 49-65 in aqueous solution containing surfactant micelles.
  Biopolymers, 33, 1877-1887.  
8497488 S.H.Bryant, and C.E.Lawrence (1993).
An empirical energy function for threading protein sequence through the folding motif.
  Proteins, 16, 92.  
1567556 A.B.Mukherjee, E.Cordella-Miele, and L.Miele (1992).
Regulation of extracellular phospholipase A2 activity: implications for inflammatory diseases.
  DNA Cell Biol, 11, 233-243.  
1623129 S.Mammi, M.T.Foffani, S.Improta, M.Tessari, E.Schievano, and E.Peggion (1992).
Conformation of uteroglobin fragments.
  Biopolymers, 32, 341-346.  
2137857 G.Camussi, C.Tetta, F.Bussolino, and C.Baglioni (1990).
Antiinflammatory peptides (antiflammins) inhibit synthesis of platelet-activating factor, neutrophil aggregation and chemotaxis, and intradermal inflammatory reactions.
  J Exp Med, 171, 913-927.  
  2398899 J.A.Lees, S.E.Fawell, R.White, and M.G.Parker (1990).
A 22-amino-acid peptide restores DNA-binding activity to dimerization-defective mutants of the estrogen receptor.
  Mol Cell Biol, 10, 5529-5531.  
2753043 N.Jamin, P.Roy, F.Fridlansky, M.Delepierre, E.Milgrom, B.P.Roques, and J.P.Mornon (1989).
Preliminary assignments of the aromatic and some methyl group resonances of the 1H-NMR spectrum of the oxidized form of uteroglobin. Application to the interaction of oxidized uteroglobin with progesterone.
  Eur J Biochem, 183, 219-226.  
3135552 J.L.De Coen, M.Deboeck, C.Delcroix, J.F.Lontie, and C.L.Malmendier (1988).
Proposed folding pattern for apolipoprotein A-II based on a structural analogy with uteroglobin.
  Proc Natl Acad Sci U S A, 85, 5669-5672.  
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 code is shown on the right.