3WJA | pdb_00003wja

The crystal structure of human cytosolic NADP(+)-dependent malic enzyme in apo form

• PDB DOI: https://doi.org/10.2210/pdb3WJA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-08 Released: 2014-08-13 
• Deposition Author(s): Li, S.-Y., Chen, M.-C., Yang, P.-C., Chan, N.-L., Liu, J.-H., Hung, H.-C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structural characteristics of the nonallosteric human cytosolic malic enzyme.

Hsieh, J.Y., Li, S.Y., Chen, M.C., Yang, P.C., Chen, H.Y., Chan, N.L., Liu, J.H., Hung, H.C.

(2014) Biochim Biophys Acta 1844: 1773-1783

• PubMed: 24998673 
• DOI: https://doi.org/10.1016/j.bbapap.2014.06.019
• Primary Citation Related Structures: 
  3WJA


• PubMed Abstract: 
  

  Human cytosolic NADP(+)-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme, whereas mitochondrial NAD(P)(+)-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate. This study examines the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME and c-NADP-ME. Multiple residues corresponding to the fumarate-binding site were mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME. Additionally, the crystal structure of the apo (ligand-free) human c-NADP-ME conformation was determined. Kinetic studies indicated no significant difference between the wild-type and mutant enzymes in Km,NADP, Km,malate, and kcat. A chimeric enzyme, [51-105]_c-NADP-ME, was designed to include the putative fumarate-binding site of m-NAD(P)-ME at the dimer interface of c-NADP-ME; however, this chimera remained nonallosteric. In addition to fumarate activation, the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME is quite different; c-NADP-ME is a stable tetramer, whereas m-NAD(P)-ME exists in equilibrium between a dimer and a tetramer. The quaternary structures for the S57K/N59E/E73K/S102D and S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G mutants of c-NADP-ME are tetrameric, whereas the K57S/E59N/K73E/D102S m-NAD(P)-ME quadruple mutant is primarily monomeric with some dimer formation. These results strongly suggest that the structural features near the fumarate-binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. In this study, we attempt to delineate the structural features governing the fumarate-induced allosteric activation of malic enzyme.

---

Organizational Affiliation: 
• Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan.
Biotechnology Center, NCHU, Taichung, Taiwan.
Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University (NTU), Taipei, Taiwan. Electronic address: [e-mail].
Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan; Institute of Genomics and Bioinformatics, NCHU, Taichung, Taiwan; Agricultural Biotechnology Center (ABC), NCHU, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, NCHU, Taichung, Taiwan. Electronic address: [e-mail].
Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan; Institute of Genomics and Bioinformatics, NCHU, Taichung, Taiwan; Agricultural Biotechnology Center (ABC), NCHU, Taichung, Taiwan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 130.59 kDa 
• Atom Count: 9,139 
• Modeled Residue Count: 1,125 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent malic enzyme	A, B	580	Homo sapiens	Mutation(s): 0  Gene Names: ME1 EC: 1.1.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P48163 (Homo sapiens) Explore P48163  Go to UniProtKB:  P48163
PHAROS:  P48163 GTEx:  ENSG00000065833

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.213	α = 90
b = 116.138	β = 90
c = 182.403	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Li, S.-Y., Chen, M.-C., Yang, P.-C., Chan, N.-L., Liu, J.-H., Hung, H.-C.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description