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 

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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: 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxypropionyl-coenzyme A dehydrataseA, B, C, D, E, F259Metallosphaera 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
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] , S [auth C] , T [auth C] , X [auth D] , 
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] , K [auth A] , O [auth B] , R [auth C] , 
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-02-07 
  • Released Date: 2018-08-01 
  • Deposition Author(s): Lee, D., Kim, K.J.

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