1UZB | pdb_00001uzb

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1UZB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-09 Released: 2004-03-11 
• Deposition Author(s): Tahirov, T.H., Inagaki, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.190 (Depositor) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase.

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

(2006) J Mol Biology 362: 490

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


• 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 114.93 kDa 
• Atom Count: 9,654 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE	A, B	516	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.2.1.88
UniProt
Find proteins for P83849 (Thermus thermophilus) Explore P83849  Go to UniProtKB:  P83849

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.190 (Depositor) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.285	α = 90
b = 102.285	β = 90
c = 279.283	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-11 
Deposition Author(s): Tahirov, T.H., Inagaki, E.

Revision History  

• Version 1.0: 2004-03-11
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description