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Oxidoreductase PDB id
2ahr
Jmol
Contents
Protein chains
257 a.a. *
Ligands
NAP ×5
FMT ×5
Metals
_NA ×5
Waters ×668
* Residue conservation analysis
PDB id:
2ahr
Name: Oxidoreductase
Title: Crystal structures of 1-pyrroline-5-carboxylate reductase fr pathogen streptococcus pyogenes
Structure: Putative pyrroline carboxylate reductase. Chain: a, b, c, d, e. Engineered: yes
Source: Streptococcus pyogenes. Organism_taxid: 160490. Strain: m1 gas. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.15Å     R-factor:   0.175     R-free:   0.210
Authors: B.Nocek,L.Lezondra,D.Holzle,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)
Key ref:
B.Nocek et al. (2005). Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes. J Mol Biol, 354, 91. PubMed id: 16233902 DOI: 10.1016/j.jmb.2005.08.036
Date:
28-Jul-05     Release date:   13-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9A1S9  (Q9A1S9_STRP1) -  Putative pyrroline carboxylate reductase
Seq:
Struc: 		256 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.1.2  - Pyrroline-5-carboxylate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Proline Biosynthesis
      Reaction: L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
L-proline
 +
NAD(P)(+)
Bound ligand (Het Group name = NAP)
corresponds exactly 		= 1-pyrroline-5-carboxylate
 + NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.08.036 J Mol Biol 354:91 (2005)
PubMed id: 16233902  
 
 
Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes.
B.Nocek, C.Chang, H.Li, L.Lezondra, D.Holzle, F.Collart, A.Joachimiak.
 
  ABSTRACT  
 
L-proline is an amino acid that plays an important role in proteins uniquely contributing to protein folding, structure, and stability, and this amino acid serves as a sequence-recognition motif. Proline biosynthesis can occur via two pathways, one from glutamate and the other from arginine. In both pathways, the last step of biosynthesis, the conversion of delta1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by delta1-pyrroline-5-carboxylate reductase (P5CR) using NAD(P)H as a cofactor. We have determined the first crystal structure of P5CR from two human pathogens, Neisseria meningitides and Streptococcus pyogenes, at 2.0 angstroms and 2.15 angstroms resolution, respectively. The catalytic unit of P5CR is a dimer composed of two domains, but the biological unit seems to be species-specific. The N-terminal domain of P5CR is an alpha/beta/alpha sandwich, a Rossmann fold. The C-terminal dimerization domain is rich in alpha-helices and shows domain swapping. Comparison of the native structure of P5CR to structures complexed with L-proline and NADP+ in two quite different primary sequence backgrounds provides unique information about key functional features: the active site and the catalytic mechanism. The inhibitory L-proline has been observed in the crystal structure.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic representation of NADP+ interactions with the surrounding protein residues (continuous blue lines) and solvent molecules (broken black line) or hydrophobic contacts (semi-circle) in molecule A of Sp-P5CR. Distances and hydrogen bond donors and acceptors are shown as subscripts and superscripts, respectively. 		Figure 8.
Figure 8. (a) Simulated annealing26omit electron density maps (F[o] -F[c]) contoured at 2.5s (blue) around l-proline molecules in the structure of Sp-P5CR complexed with l-proline. The adenosine ring of the NADP+ molecule (green) overlaps with proposed inhibitory l-proline. The NADP+ molecule is shown in the orientation as observed in the Sp-P5CR/NADP+complex. (b) Diagram of the active site l-proline binding in Sp-P5CR. (c) Close-up view of the active center of superimposed NADP and proline-bound structures showing the relative positioning between hydride donor (C4-NADPH) and acceptor (C5).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 91-0) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20177794 G.Babnigg, and A.Joachimiak (2010).
Predicting protein crystallization propensity from protein sequence.
  J Struct Funct Genomics, 11, 71-80.  
19765976 A.Joachimiak (2009).
High-throughput crystallography for structural genomics.
  Curr Opin Struct Biol, 19, 573-584.  
18566914 B.Nocek, L.Bigelow, J.Abdullah, and A.Joachimiak (2008).
Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.
  J Struct Funct Genomics, 9, 1-6.
PDB code: 2a5z
18369526 J.J.Tanner (2008).
Structural biology of proline catabolism.
  Amino Acids, 35, 719-730.  
18461181 R.M.Ward, S.Erdin, T.A.Tran, D.M.Kristensen, A.M.Lisewski, and O.Lichtarge (2008).
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features.
  PLoS ONE, 3, e2136.  
17229734 A.Ciulli, D.Y.Chirgadze, A.G.Smith, T.L.Blundell, and C.Abell (2007).
Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change, and cooperativity.
  J Biol Chem, 282, 8487-8497.
PDB code: 2ofp
17669425 B.Nocek, E.Evdokimova, M.Proudfoot, M.Kudritska, L.L.Grochowski, R.H.White, A.Savchenko, A.F.Yakunin, A.Edwards, and A.Joachimiak (2007).
Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.
  J Mol Biol, 372, 456-469.
PDB codes: 2g9i 2phn
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.