Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 116012.01 
• Atom Count: 8176 
• Residue Count: 1032 
• Unique protein chains: 1

2BJA

Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NADH

• DOI: 10.2210/pdb2BJA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2005-02-01 Released: 2006-03-09 
• Deposition Author(s): Inagaki, E., Tahirov, T.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.212 
• R-Value Work: 0.176 

Literature

Crystal Structure of Thermus Thermophilus Delta1-Pyrroline-5-Carboxylate Dehydrogenase.

Inagaki, E., Ohshima, N., Takahashi, H., Kuroishi, C., Yokoyama, S., Tahirov, T.H.

(2006) J.Mol.Biol. 362: 490

• PubMed: 16934832 
• DOI: 10.1016/j.jmb.2006.07.048
• Primary Citation of Related Structures:  
  2IY6, 1UZB, 2BJK, 2BHQ, 2BHP


• PubMed Abstract: 
  

Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDh) plays an important role in the metabolic pathway from proline to glutamate. It irreversibly catalyzes the oxidation of glutamate-gamma-semialdehyde, the product of the non-enzymatic hydrolysis of Delta(1)-pyrroline-5-carboxylate, into glutamate with the reduction of NAD(+) into NADH. We have confirmed the P5CDh activity of the Thermus thermophilus protein TT0033 (TtP5CDh), and determined the crystal structure of the enzyme in the ligand-free form at 1.4 A resolution. To investigate the structural basis of TtP5CDh function, the TtP5CDh structures with NAD(+), with NADH, and with its product glutamate were determined at 1.8 A, 1.9 A, and 1.4 A resolution, respectively. The solved structures suggest an overall view of the P5CDh catalytic mechanism and provide insights into the P5CDh deficiencies in the case of the human type II hyperprolinemia.

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Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE	A, B	516	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0
Find proteins for Q5SI02 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SI02

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MRD	A	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
NAD	A, B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MPD	B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.212 
• R-Value Work: 0.176 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 102.007	α = 90.00
b = 102.007	β = 90.00
c = 278.319	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-01 
• Released Date: 2006-03-09 
• Deposition Author(s): Inagaki, E., Tahirov, T.H.

Revision History 

• Version 1.0: 2006-03-09
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance