spacer
spacer

PDBsum entry 2ehq

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2ehq
Jmol
Contents
Protein chains
516 a.a. *
Ligands
ACT ×4
NAP ×2
MPD ×7
Metals
_NA ×2
Waters ×1060
* Residue conservation analysis
PDB id:
2ehq
Name: Oxidoreductase
Title: Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase thermus with bound NADP
Structure: 1-pyrroline-5-carboxylate dehydrogenase. Chain: a, b. Synonym: delta1-pyrroline-5-carboxylate dehydrogenase. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.55Å     R-factor:   0.159     R-free:   0.180
Authors: E.Inagaki,K.Sakamoto,S.Yokoyama,Riken Structural Genomics/pr Initiative (Rsgi)
Key ref: E.Inagaki et al. (2007). New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 462-465. PubMed id: 17554163
Date:
07-Mar-07     Release date:   01-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SI02  (Q5SI02_THET8) -  1-pyrroline-5-carboxylate dehydrogenase
Seq:
Struc:
516 a.a.
516 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:462-465 (2007)
PubMed id: 17554163  
 
 
New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+.
E.Inagaki, N.Ohshima, K.Sakamoto, N.D.Babayeva, H.Kato, S.Yokoyama, T.H.Tahirov.
 
  ABSTRACT  
 
Delta(1)-Pyrroline-5-carboxylate dehydrogenase (P5CDh) is known to preferentially use NAD(+) as a coenzyme. The k(cat) value of Thermus thermophilus P5CDh (TtP5CDh) is four times lower for NADP(+) than for NAD(+). The crystal structure of NADP(+)-bound TtP5CDh was solved in order to study the structure-activity relationships for the coenzymes. The binding mode of NADP(+) is essentially identical to that in the previously solved NAD(+)-bound form, except for the regions around the additional 2'-phosphate group of NADP(+). The coenzyme-binding site can only accommodate this group by the rotation of a glutamate residue and subtle shifts in the main chain. The 2'-phosphate of NADP(+) increases the number of hydrogen bonds between TtP5CDh and NADP(+) compared with that between TtP5CDh and NAD(+). Furthermore, the phosphate of the bound NADP(+) would restrict the ;bending' of the coenzyme because of steric hindrance. Such bending is important for dissociation of the coenzymes. These results provide a plausible explanation of the lower turnover rate of NADP(+) compared with NAD(+).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  18931443 J.P.Schuermann, T.A.White, D.Srivastava, D.B.Karr, and J.J.Tanner (2008).
Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 949-953.  
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.