4DPL

Structure of malonyl-coenzyme A reductase from crenarchaeota in complex with NadP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase.

Demmer, U.Warkentin, E.Srivastava, A.Kockelkorn, D.Potter, M.Marx, A.Fuchs, G.Ermler, U.

(2013) J.Biol.Chem. 288: 6363-6370

  • DOI: 10.1074/jbc.M112.421263
  • Primary Citation of Related Structures:  4DPK, 4DPM

  • PubMed Abstract: 
  • Autotrophic members of the Sulfolobales (crenarchaeota) use the 3-hydroxypropionate/4-hydroxybutyrate cycle to assimilate CO2 into cell material. The product of the initial acetyl-CoA carboxylation with CO2, malonyl-CoA, is further reduced to malonic ...

    Autotrophic members of the Sulfolobales (crenarchaeota) use the 3-hydroxypropionate/4-hydroxybutyrate cycle to assimilate CO2 into cell material. The product of the initial acetyl-CoA carboxylation with CO2, malonyl-CoA, is further reduced to malonic semialdehyde by an NADPH-dependent malonyl-CoA reductase (MCR); the enzyme also catalyzes the reduction of succinyl-CoA to succinic semialdehyde onwards in the cycle. Here, we present the crystal structure of Sulfolobus tokodaii malonyl-CoA reductase in the substrate-free state and in complex with NADP(+) and CoA. Structural analysis revealed an unexpected reaction cycle in which NADP(+) and CoA successively occupy identical binding sites. Both coenzymes are pressed into an S-shaped, nearly superimposable structure imposed by a fixed and preformed binding site. The template-governed cofactor shaping implicates the same binding site for the 3'- and 2'-ribose phosphate group of CoA and NADP(+), respectively, but a different one for the common ADP part: the β-phosphate of CoA aligns with the α-phosphate of NADP(+). Evolution from an NADP(+) to a bispecific NADP(+) and CoA binding site involves many amino acid exchanges within a complex process by which constraints of the CoA structure also influence NADP(+) binding. Based on the paralogous aspartate-β-semialdehyde dehydrogenase structurally characterized with a covalent Cys-aspartyl adduct, a malonyl/succinyl group can be reliably modeled into MCR and discussed regarding its binding mode, the malonyl/succinyl specificity, and the catalyzed reaction. The modified polypeptide surrounding around the absent ammonium group in malonate/succinate compared with aspartate provides the structural basis for engineering a methylmalonyl-CoA reductase applied for biotechnical polyester building block synthesis.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, D-60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malonyl-CoA/succinyl-CoA reductase
A, B, C, D
359Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Gene Names: mcr (scr)
EC: 1.2.1.75
Find proteins for Q96YK1 (Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q96YK1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.580α = 90.00
b = 128.800β = 90.00
c = 140.370γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references
  • Version 1.2: 2013-03-20
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary