PDBsum entry 3cpo

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Isomerase PDB id
Protein chain
122 a.a. *
Waters ×73
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of ketosteroid isomerase d40n with bound 2-fluorophenol
Structure: Delta(5)-3-ketosteroid isomerase. Chain: a. Synonym: steroid delta-isomerase. Engineered: yes. Mutation: yes
Source: Pseudomonas putida. Organism_taxid: 303. Gene: ksi. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.24Å     R-factor:   0.168     R-free:   0.200
Authors: J.M.M.Caaveiro,B.Pybus,D.Ringe,G.Petsko
Key ref: P.A.Sigala et al. (2008). Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc, 130, 13696-13708. PubMed id: 18808119
31-Mar-08     Release date:   23-Sep-08    
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Protein chain
Pfam   ArchSchema ?
P07445  (SDIS_PSEPU) -  Steroid Delta-isomerase
131 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transport   3 terms 
  Biochemical function     isomerase activity     2 terms  


J Am Chem Soc 130:13696-13708 (2008)
PubMed id: 18808119  
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, D.Herschlag.
Enzymes are classically proposed to accelerate reactions by binding substrates within active-site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1-1 A scale of most substrate rearrangements. The flexibility of active-site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together 1.2-1.5 A resolution X-ray crystallography, (1)H and (19)F NMR spectroscopy, quantum mechanical calculations, and transition-state analogue binding measurements to test the distance scale on which noncovalent forces can constrain the structural relaxation or translation of side chains and ligands along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side-chain reorientation and prevent hydrogen bond shortening by 0.1 A or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21365689 D.Armenta-Medina, E.Pérez-Rueda, and L.Segovia (2011).
Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches.
  Proteins, 79, 1662-1671.  
21408011 S.H.Ackerman, and D.L.Gatti (2011).
The contribution of coevolving residues to the stability of KDO8P synthase.
  PLoS One, 6, e17459.  
20080683 D.A.Kraut, P.A.Sigala, T.D.Fenn, and D.Herschlag (2010).
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.
  Proc Natl Acad Sci U S A, 107, 1960-1965.
PDB code: 3ipt
20603363 J.C.Brookes (2010).
Science is perception: what can our sense of smell tell us about ourselves and the world around us?
  Philos Transact A Math Phys Eng Sci, 368, 3491-3502.  
20133749 K.L.Peña, S.E.Castel, Araujo, G.S.Espie, and M.S.Kimber (2010).
Structural basis of the oxidative activation of the carboxysomal gamma-carbonic anhydrase, CcmM.
  Proc Natl Acad Sci U S A, 107, 2455-2460.
PDB codes: 3kwc 3kwd 3kwe
  20099310 S.C.Kamerlin, and A.Warshel (2010).
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
  Proteins, 78, 1339-1375.  
20150513 S.C.Kamerlin, P.K.Sharma, Z.T.Chu, and A.Warshel (2010).
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization.
  Proc Natl Acad Sci U S A, 107, 4075-4080.  
  19260691 D.A.Kraut, M.J.Churchill, P.E.Dawson, and D.Herschlag (2009).
Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis.
  ACS Chem Biol, 4, 269-273.  
19799395 D.K.Chakravorty, A.V.Soudackov, and S.Hammes-Schiffer (2009).
Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics.
  Biochemistry, 48, 10608-10619.  
19180666 E.Di Cera (2009).
Serine proteases.
  IUBMB Life, 61, 510-515.  
19297237 J.Damborsky, and J.Brezovsky (2009).
Computational tools for designing and engineering biocatalysts.
  Curr Opin Chem Biol, 13, 26-34.  
19706511 J.P.Schwans, D.A.Kraut, and D.Herschlag (2009).
Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase.
  Proc Natl Acad Sci U S A, 106, 14271-14275.  
19470452 P.A.Sigala, M.A.Tsuchida, and D.Herschlag (2009).
Hydrogen bond dynamics in the active site of photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 9232-9237.  
18987728 A.J.Kirby, and F.Hollfelder (2008).
Biochemistry: Enzymes under the nanoscope.
  Nature, 456, 45-47.  
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.