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PDBsum entry 1c1e
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protein ligands Protein-protein interface(s) links
Immune system PDB id
1c1e

 

 

 

 

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Contents
Protein chains
216 a.a. *
219 a.a. *
Ligands
MLT
ENH
Waters ×195
* Residue conservation analysis
PDB id:
1c1e
Name: Immune system
Title: Crystal structure of a diels-alderase catalytic antibody 1e9 in complex with its hapten
Structure: Catalytic antibody 1e9 (light chain). Chain: l. Fragment: fab fragment. Catalytic antibody 1e9 (heavy chain). Chain: h. Fragment: fab fragment
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.239     R-free:   0.294
Authors: J.Xu,I.A.Wilson
Key ref:
J.Xu et al. (1999). Evolution of shape complementarity and catalytic efficiency from a primordial antibody template. Science, 286, 2345-2348. PubMed id: 10600746 DOI: 10.1126/science.286.5448.2345
Date:
22-Jul-99     Release date:   01-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 216 a.a.
Protein chain
No UniProt id for this chain
Struc: 219 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1126/science.286.5448.2345 Science 286:2345-2348 (1999)
PubMed id: 10600746  
 
 
Evolution of shape complementarity and catalytic efficiency from a primordial antibody template.
J.Xu, Q.Deng, J.Chen, K.N.Houk, J.Bartek, D.Hilvert, I.A.Wilson.
 
  ABSTRACT  
 
The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Electron density for the hapten in the 1E9 binding pocket. The F[o] F[c] omit map contoured at 1.0 level is shown as a close-up view looking down into the antibody combining site. The solvent-exposed linker of the hapten is not shown because of disorder. Figure prepared with QUANTA [Molecular Simulations Inc. (MSI)]. 		Figure 3.
Fig. 3. Comparison of molecular surfaces of the related antibody combining sites. View is from the top of the binding site showing the fit of the cognate ligands of 1E9 (A), 39-A11 (15) (B), and DB3 (14) (C). In magenta, under the surface, the side chains of the ligand-contacting residues of each antibody are shown. Note the variation of the shape of the binding site of 1E9 due to the side-chain conformational change in TrpH50 that results from the framework TrpH47 Leu substitution. Also, the AsnH35 hydrogen bond with a ligand carbonyl oxygen is conserved in all three antibody combining sites. Figure prepared with Insight II (MSI).
 
  The above figures are reprinted by permission from the AAAs: Science (1999, 286, 2345-2348) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20877571 N.Gul, L.A.Smith, and S.A.Ahmed (2010).
Light chain separated from the rest of the type a botulinum neurotoxin molecule is the most catalytically active form.
  PLoS One, 5, e12872.  
19641790 A.J.Sinclair, V.del Amo, and D.Philp (2009).
Structure-reactivity relationships in a recognition mediated [3+2] dipolar cycloaddition reaction.
  Org Biomol Chem, 7, 3308-3318.  
19301315 C.Li, K.E.Roege, and W.L.Kelly (2009).
Analysis of the indanomycin biosynthetic gene cluster from Streptomyces antibioticus NRRL 8167.
  Chembiochem, 10, 1064-1072.  
18501202 M.Patek, and M.Drew (2008).
Chemical synthesis in nanosized cavities.
  Curr Opin Chem Biol, 12, 332-339.  
18689687 P.Verdino, C.Aldag, D.Hilvert, and I.A.Wilson (2008).
Closely related antibody receptors exploit fundamentally different strategies for steroid recognition.
  Proc Natl Acad Sci U S A, 105, 11725-11730.
PDB codes: 2o5x 2o5y 2o5z
19039353 W.L.Kelly (2008).
Intramolecular cyclizations of polyketide biosynthesis: mining for a "Diels-Alderase"?
  Org Biomol Chem, 6, 4483-4493.  
17457413 J.M.Serafimov, H.C.Lehmann, H.Oikawa, and D.Hilvert (2007).
Active site mutagenesis of the putative Diels-Alderase macrophomate synthase.
  Chem Commun (Camb), (), 1701-1703.  
16882990 M.He, M.Hamon, H.Liu, A.L.Corper, and M.J.Taussig (2006).
Effects of mutation at the D-JH junction on affinity, specificity, and idiotypy of anti-progesterone antibody DB3.
  Protein Sci, 15, 2141-2148.  
16260754 J.J.Agresti, B.T.Kelly, A.Jäschke, and A.D.Griffiths (2005).
Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization.
  Proc Natl Acad Sci U S A, 102, 16170-16175.  
15744318 J.N.Pitt, and A.R.Ferré-D'Amaré (2005).
How RNA closes a Diel.
  Nat Struct Mol Biol, 12, 206-208.  
15657969 K.C.Nicolaou, H.Xu, and M.Wartmann (2005).
Biomimetic total synthesis of gambogin and rate acceleration of pericyclic reactions in aqueous media.
  Angew Chem Int Ed Engl, 44, 756-761.  
16003810 V.Gouverneur, and M.Reiter (2005).
Biocatalytic approaches to hetero-Diels-Alder adducts of carbonyl compounds.
  Chemistry, 11, 5806-5815.  
15185369 A.Piatesi, and D.Hilvert (2004).
Immunological optimization of a generic hydrophobic pocket for high affinity hapten binding and Diels-Alder activity.
  Chembiochem, 5, 460-466.  
15213379 T.Ose, K.Watanabe, M.Yao, M.Honma, H.Oikawa, and I.Tanaka (2004).
Structure of macrophomate synthase.
  Acta Crystallogr D Biol Crystallogr, 60, 1187-1197.  
12634789 T.Ose, K.Watanabe, T.Mie, M.Honma, H.Watanabe, M.Yao, H.Oikawa, and I.Tanaka (2003).
Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase.
  Nature, 422, 185-189.
PDB code: 1izc
12093912 M.Hugot, N.Bensel, M.Vogel, M.T.Reymond, B.Stadler, J.L.Reymond, and U.Baumann (2002).
A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.
  Proc Natl Acad Sci U S A, 99, 9674-9678.
PDB codes: 1lo0 1lo2 1lo3 1lo4
11468355 B.O.Brandsdal, J.Aqvist, and A.O.Smalås (2001).
Computational analysis of binding of P1 variants to trypsin.
  Protein Sci, 10, 1584-1595.  
11410373 D.J.Tantillo, and K.N.Houk (2001).
Canonical binding arrays as molecular recognition elements in the immune system: tetrahedral anions and the ester hydrolysis transition state.
  Chem Biol, 8, 535-545.  
11948875 G.Pohnert (2001).
Diels-Alderases.
  Chembiochem, 2, 873-875.  
10760259 A.Karlstrom, G.Zhong, C.Rader, N.A.Larsen, A.Heine, R.Fuller, B.List, F.Tanaka, I.A.Wilson, C.F.Barbas, and R.A.Lerner (2000).
Using antibody catalysis to study the outcome of multiple evolutionary trials of a chemical task.
  Proc Natl Acad Sci U S A, 97, 3878-3883.  
11114507 B.Golinelli-Pimpaneau (2000).
Novel reactions catalysed by antibodies.
  Curr Opin Struct Biol, 10, 697-708.  
10966475 D.Hilvert (2000).
Critical analysis of antibody catalysis.
  Annu Rev Biochem, 69, 751-793.  
11828417 J.Chen, Q.Deng, R.Wang, K.Houk, and D.Hilvert (2000).
Shape complementarity, binding-site dynamics, and transition state stabilization: a theoretical study of Diels-Alder catalysis by antibody 1E9.
  Chembiochem, 1, 255-261.  
11114374 V.Manivel, N.C.Sahoo, D.M.Salunke, and K.V.Rao (2000).
Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site.
  Immunity, 13, 611-620.  
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.

 

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