4C3X

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 2.0 of the entry. See complete history


Literature

Crystal Structure and Site-Directed Mutagenesis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1 Explain its Catalytic Mechanism

Rohman, A.Van Oosterwijk, N.Thunnissen, A.M.W.H.Dijkstra, B.W.

(2013) J Biol Chem 288: 35559

  • DOI: 10.1074/jbc.M113.522771
  • Primary Citation of Related Structures:  
    4C3X, 4C3Y

  • PubMed Abstract: 
  • 3-Ketosteroid Δ(1)-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 Å resolution crystal structure of the 56-kDa enzyme from Rhodococcus erythropolis SQ1 (Δ(1)-KSTD1) ...

    3-Ketosteroid Δ(1)-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 Å resolution crystal structure of the 56-kDa enzyme from Rhodococcus erythropolis SQ1 (Δ(1)-KSTD1). The enzyme contains two domains: an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 Å resolution structure of Δ(1)-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues: Tyr(119), Tyr(318), Tyr(487), and Gly(491). Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr(318), respectively, whereas the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr(487) and the backbone amide of Gly(491). Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism in which Tyr(487) and Gly(491) work in tandem to promote keto-enol tautomerization and increase the acidity of the C2 hydrogen atoms of the substrate. With assistance of Tyr(119), the general base Tyr(318) abstracts the axial β-hydrogen from C2 as a proton, whereas the FAD accepts the axial α-hydrogen from the C1 atom of the substrate as a hydride ion.


    Related Citations: 
    • Purification, Crystallization and Preliminary X-Ray Crystallographic Analysis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1
      Rohman, A., Van Oosterwijk, N., Dijkstra, B.W.
      (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 551

    Organizational Affiliation

    From the Department of Chemistry, Faculty of Sciences and Technology and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-KETOSTEROID DEHYDROGENASEA, B, C, D, E, F, G, H530Rhodococcus erythropolisMutation(s): 0 
Gene Names: kstD1BS297_24040rerp_49010RERY_47440
EC: 1.3.99.4
Find proteins for Q9RA02 (Rhodococcus erythropolis)
Explore Q9RA02 
Go to UniProtKB:  Q9RA02
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
I, J, K, L, M, N, O, P
I, J, K, L, M, N, O, P, Q, R, S, T
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth B], DB [auth H], FA [auth C], KA [auth D], OA [auth E], U [auth A], UA [auth F], YA [auth G]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BB [auth G] , CA [auth B] , CB [auth G] , DA [auth B] , EA [auth B] , FB [auth H] , GB [auth H] , IA [auth C] , 
BB [auth G],  CA [auth B],  CB [auth G],  DA [auth B],  EA [auth B],  FB [auth H],  GB [auth H],  IA [auth C],  JA [auth C],  MA [auth D],  NA [auth D],  RA [auth E],  SA [auth E],  TA [auth E],  WA [auth F],  X [auth A],  XA [auth F],  Y [auth A],  Z [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth G], BA [auth B], EB [auth H], HA [auth C], LA [auth D], QA [auth E], VA [auth F], W [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth C], PA [auth E], V [auth A], ZA [auth G]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
I, J, K, L, M, N, O, P, Q, R, S, TsucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.385α = 90
b = 131.625β = 90
c = 363.161γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary