spacer
spacer

PDBsum entry 3i1c
Go to PDB code: 
protein ligands links
Hydrolase PDB id
3i1c

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
314 a.a. *
Ligands
GOL
Waters ×348
* Residue conservation analysis
PDB id:
3i1c
Name: Hydrolase
Title: Crystal structure of a novel engineered diels-alderase: da_20_00_a74i
Structure: Diisopropyl-fluorophosphatase. Chain: a. Synonym: dfpase. Engineered: yes. Mutation: yes
Source: Loligo vulgaris. Common european squid. Organism_taxid: 6622. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.188     R-free:   0.253
Authors: A.R.Lambert,B.L.Stoddard
Key ref: J.B.Siegel et al. (2010). Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science, 329, 309-313. PubMed id: 20647463
Date:
26-Jun-09     Release date:   18-Aug-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7SIG4  (DFPA_LOLVU) -  Diisopropyl-fluorophosphatase from Loligo vulgaris
Seq:
Struc: 		314 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.8.2  - Transferred entry: 3.8.2.2.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: diisopropyl fluorophosphate + H2O = diisopropyl phosphate + fluoride + 2 H+
diisopropyl fluorophosphate
 + H2O
 = diisopropyl phosphate
 + fluoride
 + 2 × H(+)
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Science 329:309-313 (2010)
PubMed id: 20647463  
 
 
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
J.B.Siegel, A.Zanghellini, H.M.Lovick, G.Kiss, A.R.Lambert, J.L.St Clair, J.L.Gallaher, D.Hilvert, M.H.Gelb, B.L.Stoddard, K.N.Houk, F.E.Michael, D.Baker.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23135467 N.Koga, R.Tatsumi-Koga, G.Liu, R.Xiao, T.B.Acton, G.T.Montelione, and D.Baker (2012).
Principles for designing ideal protein structures.
  Nature, 491, 222-227.
PDB codes: 2kl8 2ln3 2lta 2lv8 2lvb
22575958 U.T.Bornscheuer, G.W.Huisman, R.J.Kazlauskas, S.Lutz, J.C.Moore, and K.Robins (2012).
Engineering the third wave of biocatalysis.
  Nature, 485, 185-194.  
21349882 A.Morin, K.W.Kaufmann, C.Fortenberry, J.M.Harp, L.S.Mizoue, and J.Meiler (2011).
Computational design of an endo-1,4-{beta}-xylanase ligand binding site.
  Protein Eng Des Sel, 24, 503-516.
PDB codes: 3mf6 3mf9 3mfa 3mfc
21115265 A.S.Bommarius, J.K.Blum, and M.J.Abrahamson (2011).
Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst.
  Curr Opin Chem Biol, 15, 194-200.  
21195018 B.M.Nestl, B.A.Nebel, and B.Hauer (2011).
Recent progress in industrial biocatalysis.
  Curr Opin Chem Biol, 15, 187-193.  
21185770 E.M.Brustad, and F.H.Arnold (2011).
Optimizing non-natural protein function with directed evolution.
  Curr Opin Chem Biol, 15, 201-210.  
21157606 H.S.Rzepa (2011).
Can 1,3-dimethylcyclobutadiene and carbon dioxide co-exist inside a supramolecular cavity?
  Chem Commun (Camb), 47, 1851-1853.  
21258712 J.T.MacDonald, C.Barnes, R.I.Kitney, P.S.Freemont, and G.B.Stan (2011).
Computational design approaches and tools for synthetic biology.
  Integr Biol (Camb), 3, 97.  
21064163 M.M.Stratton, and S.N.Loh (2011).
Converting a protein into a switch for biosensing and functional regulation.
  Protein Sci, 20, 19-29.  
  21480401 P.J.Deuss, R.den Heeten, W.Laan, and P.C.Kamer (2011).
Bioinspired catalyst design and artificial metalloenzymes.
  Chemistry, 17, 4680-4698.  
21369567 Y.Mo, P.Bao, and J.Gao (2011).
Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory.
  Phys Chem Chem Phys, 13, 6760-6775.  
20827800 A.Doerr (2010).
Molecular engineering: Unnatural design.
  Nat Methods, 7, 671.  
21052559 B.R.Fritz, L.E.Timmerman, N.M.Daringer, J.N.Leonard, and M.C.Jewett (2010).
Biology by design: from top to bottom and back.
  J Biomed Biotechnol, 2010, 232016.  
20850962 C.Jäckel, and D.Hilvert (2010).
Biocatalysts by evolution.
  Curr Opin Biotechnol, 21, 753-759.  
20717908 D.Baker (2010).
An exciting but challenging road ahead for computational enzyme design.
  Protein Sci, 19, 1817-1819.  
20665693 G.Kiss, D.Röthlisberger, D.Baker, and K.N.Houk (2010).
Evaluation and ranking of enzyme designs.
  Protein Sci, 19, 1760-1773.  
21127247 J.D.Keasling (2010).
Manufacturing molecules through metabolic engineering.
  Science, 330, 1355-1358.  
21057692 M.Harmata (2010).
The (4+3)-cycloaddition reaction: simple allylic cations as dienophiles.
  Chem Commun (Camb), 46, 8886-8903.  
20647454 S.Lutz (2010).
Biochemistry. Reengineering enzymes.
  Science, 329, 285-287.  
20869867 S.Lutz (2010).
Beyond directed evolution--semi-rational protein engineering and design.
  Curr Opin Biotechnol, 21, 734-743.  
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