1PJL | pdb_00001pjl

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 (Depositor) 
  • R-Value Work: 
    0.204 (Depositor) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PJL

This is version 1.4 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: https://doi.org/10.1006/bbrc.2000.3163
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 541.81 kDa 
  • Atom Count: 35,527 
  • Modeled Residue Count: 4,408 
  • Deposited Residue Count: 4,672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent malic enzyme, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H
584Homo 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
GTEx:  ENSG00000082212 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23368
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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]
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
LU

Query on LU



Download:Ideal Coordinates CCD File
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.263 (Depositor) 
  • R-Value Work:  0.204 (Depositor) 
  • R-Value Observed: 0.204 (Depositor) 
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
  • Version 1.4: 2024-10-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary