5ZAI

Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula

Lee, D.Kim, K.J.

(2018) Sci Rep 8: 10692-10692

  • DOI: https://doi.org/10.1038/s41598-018-29070-w
  • Primary Citation of Related Structures:  
    5ZAI

  • PubMed Abstract: 
  • Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA ...

    Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA. To elucidate the molecular mechanism of 3HPCD from M. sedula (Ms3HPCD), we determined its crystal structure in complex with Coenzyme A (CoA). Ms3HPCD showed an overall structure and the CoA-binding mode similar to other enoyl-CoA hydratase (ECH) family enzymes. However, compared with the other ECHs, Ms3HPCD has a tightly formed α3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short-chain 3-hydroxyacyl-CoA as a substrate. Moreover, based on the phylogenetic tree analysis, we propose that the 3HPCD homologues from the phylum Crenarchaeota have an enoyl-group binding pocket similar to that of bacterial short-chain ECHs.


    Organizational Affiliation

    KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea. kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxypropionyl-coenzyme A dehydratase
A, B, C, D, E
A, B, C, D, E, F
259Metallosphaera sedula DSM 5348Mutation(s): 0 
Gene Names: Msed_2001
EC: 4.2.1.116
UniProt
Find proteins for A4YI89 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2))
Explore A4YI89 
Go to UniProtKB:  A4YI89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4YI89
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
AA [auth E],
G [auth A],
N [auth B],
Q [auth C]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
L [auth A]
M [auth A]
P [auth B]
BA [auth E],
EA [auth F],
L [auth A],
M [auth A],
P [auth B],
S [auth C],
T [auth C],
X [auth D],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
H [auth A]
I [auth A]
J [auth A]
CA [auth F],
DA [auth F],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
R [auth C],
U [auth D],
V [auth D],
W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.685α = 90
b = 130.17β = 119.57
c = 84.791γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Structure summary