5HZ2

Crystal structure of PhaC1 from Ralstonia eutropha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms.

Kim, J.Kim, Y.J.Choi, S.Y.Lee, S.Y.Kim, K.J.

(2017) Biotechnol J 12

  • DOI: 10.1002/biot.201600648
  • Primary Citation of Related Structures:  
    5HZ2

  • PubMed Abstract: 
  • Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. Here, we report the first crystal structure of Ralstonia eutropha PHA synthase at 1 ...

    Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. Here, we report the first crystal structure of Ralstonia eutropha PHA synthase at 1.8 Å resolution and structure-based mechanisms for PHA polymerization. RePhaC1 contains two distinct domains, the N-terminal (RePhaC1 ND ) and C-terminal domains (RePhaC1 CD ), and exists as a dimer. RePhaC1 CD catalyzes polymerization via non-processive ping-pong mechanism using a Cys-His-Asp catalytic triad. Molecular docking simulation of 3-hydroxybutyryl-CoA to the active site of RePhaC1 CD reveals residues involved in the formation of 3-hydroxybutyryl-CoA binding pocket and substrate binding tunnel. Comparative analysis with other polymerases elucidates how different classes of PHA synthases show different substrate specificities. Furthermore, we attempted structure-based protein engineering and developed a RePhaC1 mutant with enhanced PHA synthase activity.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly-beta-hydroxybutyrate polymeraseA396Cupriavidus necator H16Mutation(s): 0 
Gene Names: phbCH16_A1437phaC
EC: 2.3.1
UniProt
Find proteins for P23608 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore P23608 
Go to UniProtKB:  P23608
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23608
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.246α = 90
b = 87.856β = 90
c = 136.479γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2016-02-02 
  • Released Date: 2016-12-07 
  • Deposition Author(s): Kim, J., Kim, K.-J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references