8I70 | pdb_00008i70

Crystal structure of NADP-binding form of malonyl-CoA reductase C-domain from Chloroflexus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.191 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of bifunctional malonyl-CoA reductase from Chloroflexus aurantiacus reveals a dynamic domain movement for high enzymatic activity.

Ahn, J.W.Kim, S.Hong, J.Kim, K.J.

(2023) Int J Biol Macromol 242: 124676-124676

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.124676
  • Primary Citation Related Structures: 
    8HJW, 8I6Z, 8I70

  • PubMed Abstract: 

    The platform chemical 3-hydroxypropionic acid is used to synthesize various valuable materials, including bioplastics. Bifunctional malonyl-CoA reductase is a key enzyme in 3-hydroxypropionic acid biosynthesis as it catalyzes the two-step reduction of malonyl-CoA to malonate semialdehyde to 3-hydroxypropionic acid. Here, we report the cryo-EM structure of a full-length malonyl-CoA reductase protein from Chloroflexus aurantiacus (CaMCR Full ). The EM model of CaMCR Full reveals a tandem helix architecture comprising an N-terminal (CaMCR ND ) and a C-terminal (CaMCR CD ) domain. The CaMCR Full model also revealed that the enzyme undergoes a dynamic domain movement between CaMCR ND and CaMCR CD due to the presence of a flexible linker between these two domains. Increasing the flexibility and extension of the linker resulted in a twofold increase in enzyme activity, indicating that for CaMCR, domain movement is crucial for high enzyme activity. We also describe the structural features of CaMCR ND and CaMCR CD . This study reveals the protein structures underlying the molecular mechanism of CaMCR Full and thereby provides valuable information for future enzyme engineering to improve the productivity of 3-hydroxypropionic acid.


  • Organizational Affiliation
    • Postech Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Center for Biomolecular Capture Technology, Bio Open Innovation Center, Pohang University of Science and Technology, 47 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 76.64 kDa 
  • Atom Count: 5,644 
  • Modeled Residue Count: 658 
  • Deposited Residue Count: 689 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase/reductase SDR689Chloroflexus aurantiacusMutation(s): 0 
Gene Names: Caur_2614
EC: 1.2.1.75
UniProt
Find proteins for A9WIU3 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WIU3 
Go to UniProtKB:  A9WIU3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WIU3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.191 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.675α = 90
b = 139.644β = 97.71
c = 73.565γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection