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Isomerase PDB id
3dh7
Jmol
Contents
Protein chains
318 a.a. *
Ligands
FMN ×4
POP ×2
Waters ×229
* Residue conservation analysis
PDB id:
3dh7
Name: Isomerase
Title: Structure of t. Thermophilus idi-2 in complex with ppi
Structure: Isopentenyl-diphosphate delta-isomerase. Chain: a, b, c, d. Engineered: yes
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Gene: tthb110. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.97Å     R-factor:   0.215     R-free:   0.293
Authors: J.De Ruyck,J.Wouters
Key ref: J.de Ruyck et al. (2008). Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate. Biochemistry, 47, 9051-9053. PubMed id: 18693754 DOI: 10.1021/bi801159x
Date:
17-Jun-08     Release date:   23-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q53W52  (Q53W52_THET8) -  Isopentenyl-diphosphate delta-isomerase
Seq:
Struc: 		332 a.a.
318 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1021/bi801159x Biochemistry 47:9051-9053 (2008)
PubMed id: 18693754  
 
 
Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate.
J.de Ruyck, J.Pouyez, S.C.Rothman, D.Poulter, J.Wouters.
 
  ABSTRACT  
 
The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase in complex with inorganic pyrophosphate, providing new insights about the active site and the catalytic mechanism of the enzyme. The PP i moiety is located near the conserved residues, H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site of isopentenyl diphosphate isomerase 2 provides interactions for stabilizing a carbocationic intermediate similar to those that stabilize the intermediate in the well-established protonation-deprotonation mechanism of isopentenyl diphosphate isomerase 1.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19158086 H.Unno, S.Yamashita, Y.Ikeda, S.Y.Sekiguchi, N.Yoshida, T.Yoshimura, M.Kusunoki, T.Nakayama, T.Nishino, and H.Hemmi (2009).
New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
  J Biol Chem, 284, 9160-9167.  
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.