1GQ2

Malic Enzyme from Pigeon Liver


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme

Yang, Z.Zhang, H.Huang, H.-C.Kuo, C.-C.Tsai, L.-C.Yuan, H.S.Chou, W.-Y.Chang, G.-G.Tong, L.

(2002) Protein Sci 11: 332

  • DOI: 10.1110/ps.38002
  • Primary Citation of Related Structures:  
    1GQ2

  • PubMed Abstract: 
  • Malic enzymes are widely distributed in nature, and have important biological functions. They catalyze the oxidative decarboxylation of malate to produce pyruvate and CO(2) in the presence of divalent cations (Mg(2+), Mn(2+)). Most malic enzymes have a clear selectivity for the dinucleotide cofactor, being able to use either NAD(+) or NADP(+), but not both ...

    Malic enzymes are widely distributed in nature, and have important biological functions. They catalyze the oxidative decarboxylation of malate to produce pyruvate and CO(2) in the presence of divalent cations (Mg(2+), Mn(2+)). Most malic enzymes have a clear selectivity for the dinucleotide cofactor, being able to use either NAD(+) or NADP(+), but not both. Structural studies of the human mitochondrial NAD(+)-dependent malic enzyme established that malic enzymes belong to a new class of oxidative decarboxylases. Here we report the crystal structure of the pigeon cytosolic NADP(+)-dependent malic enzyme, in a closed form, in a quaternary complex with NADP(+), Mn(2+), and oxalate. This represents the first structural information on an NADP(+)-dependent malic enzyme. Despite the sequence conservation, there are large differences in several regions of the pigeon enzyme structure compared to the human enzyme. One region of such differences is at the binding site for the 2'-phosphate group of the NADP(+) cofactor, which helps define the cofactor selectivity of the enzymes. Specifically, the structural information suggests Lys362 may have an important role in the NADP(+) selectivity of the pigeon enzyme, confirming our earlier kinetic observations on the K362A mutant. Our structural studies also revealed differences in the organization of the tetramer between the pigeon and the human enzymes, although the pigeon enzyme still obeys 222 symmetry.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALIC ENZYME
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
555Columba liviaMutation(s): 14 
Gene Names: ME1
EC: 1.1.1.40
UniProt
Find proteins for P40927 (Columba livia)
Explore P40927 
Go to UniProtKB:  P40927
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40927
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
AB [auth G],
BD [auth N],
FB [auth H],
FC [auth K],
HD [auth O],
AB [auth G],
BD [auth N],
FB [auth H],
FC [auth K],
HD [auth O],
IA [auth D],
KC [auth L],
NA [auth E],
OB [auth I],
PC [auth M],
Q [auth A],
SD [auth P],
T [auth B],
TA [auth F],
X [auth C],
YB [auth J]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
OXL
Query on OXL

Download Ideal Coordinates CCD File 
BB [auth G],
CD [auth N],
GB [auth H],
GC [auth K],
ID [auth O],
BB [auth G],
CD [auth N],
GB [auth H],
GC [auth K],
ID [auth O],
JA [auth D],
LC [auth L],
OA [auth E],
PB [auth I],
QC [auth M],
R [auth A],
TD [auth P],
U [auth B],
UA [auth F],
Y [auth C],
ZB [auth J]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AC [auth J],
CB [auth G],
DD [auth N],
HB [auth H],
HC [auth K],
AC [auth J],
CB [auth G],
DD [auth N],
HB [auth H],
HC [auth K],
JD [auth O],
KA [auth D],
MC [auth L],
PA [auth E],
QB [auth I],
RC [auth M],
S [auth A],
UD [auth P],
V [auth B],
VA [auth F],
Z [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AD [auth M],
AE [auth P],
BE [auth P],
CE [auth P],
DC [auth J],
AD [auth M],
AE [auth P],
BE [auth P],
CE [auth P],
DC [auth J],
EA [auth C],
EB [auth G],
EC [auth J],
FA [auth C],
FD [auth N],
GA [auth C],
GD [auth N],
HA [auth C],
JC [auth K],
NB [auth H],
OC [auth L],
OD [auth O],
PD [auth O],
QA [auth E],
QD [auth O],
RA [auth E],
RD [auth O],
SA [auth E],
TB [auth I],
UB [auth I],
VB [auth I],
W [auth B],
WB [auth I],
XB [auth I],
YA [auth F],
YC [auth M],
ZA [auth F],
ZC [auth M]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
BC [auth J],
CA [auth C],
CC [auth J],
AA [auth C],
BA [auth C],
BC [auth J],
CA [auth C],
CC [auth J],
DA [auth C],
DB [auth G],
ED [auth N],
IB [auth H],
IC [auth K],
JB [auth H],
KB [auth H],
KD [auth O],
LA [auth D],
LB [auth H],
LD [auth O],
MA [auth D],
MB [auth H],
MD [auth O],
NC [auth L],
ND [auth O],
RB [auth I],
SB [auth I],
SC [auth M],
TC [auth M],
UC [auth M],
VC [auth M],
VD [auth P],
WA [auth F],
WC [auth M],
WD [auth P],
XA [auth F],
XC [auth M],
XD [auth P],
YD [auth P],
ZD [auth P]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.149α = 90.05
b = 140.863β = 87.16
c = 167.079γ = 75.63
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance