PDBsum entry 2ger

Oxidoreductase

PDB id: 2ger

Contents

Protein chains

277 a.a. *

Waters ×597

* Residue conservation analysis

PDB id:

2ger

Name:

Oxidoreductase

Title:

Crystal structure and oxidative mechanism of human pyrroline-5- carboxylate reductase

Structure:

Pyrroline-5-carboxylate reductase 1. Chain: a, b, c, d, e. Synonym: p5cr 1, p5c reductase 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.10Å R-factor: 0.233 R-free: 0.261

Authors:

Z.Meng,Z.Lou,Z.Liu,Z.Rao

Key ref:

Z.Meng et al. (2006). Crystal structure of human pyrroline-5-carboxylate reductase. J Mol Biol, 359, 1364-1377. PubMed id: 16730026 DOI: 10.1016/j.jmb.2006.04.053

Date:

20-Mar-06 Release date: 19-Sep-06

Protein chains

P32322  (P5CR1_HUMAN) -  Pyrroline-5-carboxylate reductase 1, mitochondrial from Homo sapiens

Seq: 319 a.a.

Struc: 277 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.2 - pyrroline-5-carboxylate reductase.
• Pathway: Proline Biosynthesis
• Reaction:
  1. L-proline + NAD⁺ = (S)-1-pyrroline-5-carboxylate + NADH + 2 H⁺
  2. L-proline + NADP⁺ = (S)-1-pyrroline-5-carboxylate + NADPH + 2 H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2006.04.053

J Mol Biol 359:1364-1377 (2006)

PubMed id: 16730026

Crystal structure of human pyrroline-5-carboxylate reductase.

Z.Meng, Z.Lou, Z.Liu, M.Li, X.Zhao, M.Bartlam, Z.Rao.

ABSTRACT

Pyrroline-5-carboxylate reductase (P5CR) is a universal housekeeping enzyme that catalyzes the reduction of Delta(1)-pyrroline-5-carboxylate (P5C) to proline using NAD(P)H as the cofactor. The enzymatic cycle between P5C and proline is very important for the regulation of amino acid metabolism, intracellular redox potential, and apoptosis. Here, we present the 2.8 Angstroms resolution structure of the P5CR apo enzyme, its 3.1 Angstroms resolution ternary complex with NAD(P)H and substrate-analog. The refined structures demonstrate a decameric architecture with five homodimer subunits and ten catalytic sites arranged around a peripheral circular groove. Mutagenesis and kinetic studies reveal the pivotal roles of the dinucleotide-binding Rossmann motif and residue Glu221 in the human enzyme. Human P5CR is thermostable and the crystals were grown at 37 degrees C. The enzyme is implicated in oxidation of the anti-tumor drug thioproline.

Selected figure(s)

Figure 1.
Figure 1. The P5CR structure. (a) Overall view of the P5CR crystal structure. A ribbon representation of only one homodimer is shown, with each monomer presented in magenta and gold, respectively. The other four homodimers, which form the decamer, are shown in molecular surface representation. (b) The potential surface of the decamer ternary complex. The binding cofactor and substrate analog are shown as magenta spheres around the circular groove. The three dimensions are labeled and the negatively charged central channel with 25 Å diameter is shown. (c) Two views related by 90° of the monomer structure of P5CR, showing domains A and B with their secondary structure units in detail. (d) Two views related by 90° of the dimer structure of P5CR, showing how two monomers coil around each other to form one dimer. Monomers are shown in cartoon representation in magenta and gold, respectively. Secondary structure units of molecule 1 are named as αx-1; and in molecule 2 are named as αx-2. (e) Stereo view of the inter-homodimer interactions. Only two homodimers are shown at the interface. Molecules A and H, which belong to one dimer, are shown in magenta and yellow, respectively; molecules E and I, which belong to the other dimer, are drawn in green and red, respectively. There are 11 inter-homodimer, five water-mediated inter-molecular and four inntra-molecular hydrogen bonds, which form an interaction web between two homodimers. Hydrogen bonds are shown as broken cyan lines. (f) Investigation of the decamer stability with different concentrations of urea. In the Superdex200 profiles, P5CR eluted at the decamer peak when treated with no urea (black) or with 0.5 M urea (magenta). The decamer began to dissociate into dimers from 1 M urea (yellow) and 2 M urea (blue) and dissociated completely into dimers at 4 M urea (red). P5CR was refolded into a decamer from 6 M urea in Superdex200 (shown as a green curve). No monomer was observed for any concentration of urea. (g) Thermal inactivation of P5CR: (1) after incubation at various temperatures (20–75 °C) for 10 min, the relative activities of P5CR were measured at 25 °C. (2) The time-dependent thermal inactivation of P5CR was investigated at 40 °C and at 68 °C. The relative activities were measured at 25 °C and plotted against time.

Figure 3.
Figure 3. (a) Structure-based sequence alignment between P5CR in human and in different organisms as indicated. Arrows indicate β-strands; cylinders denote α-helices. Background-red residues indicate those that are conserved; background-yellow denotes residues identified to be more than 80% conserved. Residues that are important for cofactor and substrate analog binding are framed in black. (b) Superposition of P5CR from human (yellow), Neisseria meningitides Mc58 (green) and Streptococcus pyogenes (red). The α2 helix of all three structures is shown in ribbon representation and the other parts are shown as smooth lines. The NADP cofactor bound in the structure of P5CR from Streptococcus pyogenes is shown in magenta stick representation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 1364-1377) copyright 2006.