1PJL

Crystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Potent and competitive inhibition of malic enzymes by lanthanide ions

Yang, Z.Batra, R.Floyd, D.L.Hung, H.-C.Chang, G.-G.Tong, L.

(2000) Biochem Biophys Res Commun 274: 440-444

  • DOI: 10.1006/bbrc.2000.3163
  • Primary Citation of Related Structures:  
    1PJL

  • PubMed Abstract: 
  • The catalytic activity of malic enzyme (ME), a member of a new class of oxidative decarboxylases, requires the presence of divalent cations (Mn(2+), Mg(2+), and others). The crystal structure at 2.9 A resolution of human mitochondrial NAD(+)-dependent malic enzyme in a ternary complex with NAD(+) and the lanthanide ion Lu(3+), which has similar radius as Mn(2+), reveals a new conformation of the enzyme ...

    The catalytic activity of malic enzyme (ME), a member of a new class of oxidative decarboxylases, requires the presence of divalent cations (Mn(2+), Mg(2+), and others). The crystal structure at 2.9 A resolution of human mitochondrial NAD(+)-dependent malic enzyme in a ternary complex with NAD(+) and the lanthanide ion Lu(3+), which has similar radius as Mn(2+), reveals a new conformation of the enzyme. The active site in this ternary complex is in an open form, while the organization of the tetramer of the enzyme actually resembles that with a closed active site. The Lu(3+) ion is bound to the enzyme at the same site as Mn(2+). Kinetic studies showed that Lu(3+) is a potent inhibitor of both the human NAD(P)(+)-dependent ME and the NADP(+)-dependent ME from pigeon liver, and is competitive with respect to the divalent cation, consistent with the structural information.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York, 10027, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent malic enzyme, mitochondrialA, B, C, D, E, F, G, H584Homo sapiensMutation(s): 15 
Gene Names: ME2
EC: 1.1.1.38
UniProt & NIH Common Fund Data Resources
Find proteins for P23368 (Homo sapiens)
Explore P23368 
Go to UniProtKB:  P23368
PHAROS:  P23368
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
BA [auth G] , CA [auth G] , EA [auth H] , FA [auth H] , J [auth A] , K [auth A] , M [auth B] , N [auth B] , 
BA [auth G],  CA [auth G],  EA [auth H],  FA [auth H],  J [auth A],  K [auth A],  M [auth B],  N [auth B],  P [auth C],  Q [auth C],  S [auth D],  T [auth D],  V [auth E],  W [auth E],  Y [auth F],  Z [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
LU
Query on LU

Download Ideal Coordinates CCD File 
AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]LUTETIUM (III) ION
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.3α = 116.5
b = 119β = 94.8
c = 125.9γ = 102.8
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description