spacer
spacer

PDBsum entry 1omd

Go to PDB code: 
protein metals links
Calcium binding protein PDB id
1omd
Jmol
Contents
Protein chain
107 a.a. *
Metals
_CA ×3
Waters ×87
* Residue conservation analysis
PDB id:
1omd
Name: Calcium binding protein
Title: Structure of oncomodulin refined at 1.85 angstroms resolution. An example of extensive molecular aggregation via ca2+
Structure: Oncomodulin. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116
Resolution:
1.85Å     R-factor:   0.166    
Authors: F.R.Ahmed,M.Przybylska,D.R.Rose,G.I.Birnbaum,M.E.Pippy, J.P.Macmanus
Key ref: F.R.Ahmed et al. (1990). Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+. J Mol Biol, 216, 127-140. PubMed id: 2231727 DOI: 10.1016/S0022-2836(05)80065-8
Date:
19-Apr-90     Release date:   15-Jul-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02631  (ONCO_RAT) -  Oncomodulin
Seq:
Struc:
109 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   3 terms 
  Biological process     cytosolic calcium ion homeostasis   1 term 
  Biochemical function     protein homodimerization activity     4 terms  

 

 
DOI no: 10.1016/S0022-2836(05)80065-8 J Mol Biol 216:127-140 (1990)
PubMed id: 2231727  
 
 
Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+.
F.R.Ahmed, M.Przybylska, D.R.Rose, G.I.Birnbaum, M.E.Pippy, J.P.MacManus.
 
  ABSTRACT  
 
The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1.85 A resolution. For the 5770 reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin molecule. The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to seven oxygen atoms, including one water molecule. The third Ca2+ is also seven-co-ordinated, to five oxygen atoms belonging to three different oncomodulin molecules and to two water molecules which form hydrogen bonds to a fourth oncomodulin; thus, this intermolecular Ca2+ and its equivalents interlink the molecules into zigzag layers normal to the b axis with a spacing of b/2 or 32.14 A. No such extensive molecular aggregation has been reported for any of the related Ca-binding regulatory proteins of the troponin-C family studied thus far. The Ca-O distances in all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly bound Ca polyhedra.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16545112 K.A.Snyder, H.J.Feldman, M.Dumontier, J.J.Salama, and C.W.Hogue (2006).
Domain-based small molecule binding site annotation.
  BMC Bioinformatics, 7, 152.  
  10739249 R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, and D.J.Nelson (2000).
X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).
  Protein Sci, 9, 73-82.
PDB code: 1bu3
10491125 J.A.Cox, I.Durussel, D.J.Scott, and M.W.Berchtold (1999).
Remodeling of the AB site of rat parvalbumin and oncomodulin into a canonical EF-hand.
  Eur J Biochem, 264, 790-799.  
9636056 M.T.Henzl, R.C.Hapak, and J.J.Likos (1998).
Interconversion of the ligand arrays in the CD and EF sites of oncomodulin. Influence on Ca2+-binding affinity.
  Biochemistry, 37, 9101-9111.  
8816770 M.Gerstein, and C.Chothia (1996).
Packing at the protein-water interface.
  Proc Natl Acad Sci U S A, 93, 10167-10172.  
8639547 M.T.Henzl, R.C.Hapak, and E.A.Goodpasture (1996).
Introduction of a fifth carboxylate ligand heightens the affinity of the oncomodulin CD and EF sites for Ca2+.
  Biochemistry, 35, 5856-5869.  
8973640 T.L.Pauls, I.Durussel, I.D.Clark, A.G.Szabo, M.W.Berchtold, and J.A.Cox (1996).
Site-specific replacement of amino acid residues in the CD site of rat parvalbumin changes the metal specificity of this Ca2+/Mg(2+)-mixed site toward a Ca(2+)-specific site.
  Eur J Biochem, 242, 249-255.  
8611623 T.L.Pauls, J.A.Cox, and M.W.Berchtold (1996).
The Ca2+(-)binding proteins parvalbumin and oncomodulin and their genes: new structural and functional findings.
  Biochim Biophys Acta, 1306, 39-54.  
7896823 A.C.da Silva, J.Kendrick-Jones, and F.C.Reinach (1995).
Determinants of ion specificity on EF-hands sites. Conversion of the Ca2+/Mg2+ site of smooth muscle myosin regulatory light chain into a Ca(2+)-specific site.
  J Biol Chem, 270, 6773-6778.  
7552750 S.M.Gagné, S.Tsuda, M.X.Li, L.B.Smillie, and B.D.Sykes (1995).
Structures of the troponin C regulatory domains in the apo and calcium-saturated states.
  Nat Struct Biol, 2, 784-789.
PDB codes: 1tnp 1tnq
  7920247 G.S.Shaw, R.S.Hodges, C.M.Kay, and B.D.Sykes (1994).
Relative stabilities of synthetic peptide homo- and heterodimeric troponin-C domains.
  Protein Sci, 3, 1010-1019.  
8341660 M.Renner, M.A.Danielson, and J.J.Falke (1993).
Kinetic control of Ca(II) signaling: tuning the ion dissociation rates of EF-hand Ca(II) binding sites.
  Proc Natl Acad Sci U S A, 90, 6493-6497.  
8354278 U.G.Föhr, B.R.Weber, M.Müntener, W.Staudenmann, G.J.Hughes, S.Frutiger, D.Banville, B.W.Schäfer, and C.W.Heizmann (1993).
Human alpha and beta parvalbumins. Structure and tissue-specific expression.
  Eur J Biochem, 215, 719-727.  
1333989 M.T.Henzl, C.L.Treviño, L.Dvoráková, and J.M.Boschi (1992).
Evidence that deprotonation of serine-55 is responsible for the pH-dependence of the parvalbumin Eu3+ 7F0-->5D0 spectrum.
  FEBS Lett, 314, 130-134.  
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.