5FYD | pdb_00005fyd

Structural and biochemical insights into 7beta-hydroxysteroid dehydrogenase stereoselectivity

• PDB DOI: https://doi.org/10.2210/pdb5FYD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Collinsella aerofaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2016-04-06 
• Deposition Author(s): Savino, S., Ferrandi, E., Forneris, F., Rovida, S., Riva, S., Monti, D., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.209 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural and Biochemical Insights Into 7Beta-Hydroxysteroid Dehydrogenase Stereoselectivity.

Savino, S., Ferrandi, E.E., Forneris, F., Rovida, S., Riva, S., Monti, D., Mattevi, A.

(2016) Proteins 84: 859

• PubMed: 27006087 
• DOI: https://doi.org/10.1002/prot.25036
• Primary Citation Related Structures: 
  5FYD


• PubMed Abstract: 
  

  Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo- and regio-selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7β-hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active-site accessibility, the bases of the specificity for NADP(+) , and the general architecture of the steroid binding site. Comparison with 7α-hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C-terminal extension reshapes the substrate site of the β-selective enzyme, possibly leading to an inverted orientation of the bound substrate. Proteins 2016; 84:859-865. © 2016 Wiley Periodicals, Inc.

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Organizational Affiliation: 
• Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia, 27100, Italy.
Istituto di Chimica del Riconoscimento Molecolare, CNR, via Mario Bianco 9, Milano, 20131, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.66 kDa 
• Atom Count: 4,269 
• Modeled Residue Count: 511 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN	A, B	263	Collinsella aerofaciens	Mutation(s): 0  EC: 1.1.1.201
UniProt
Find proteins for A4ECA9 (Collinsella aerofaciens (strain ATCC 25986 / DSM 3979 / JCM 10188 / KCTC 3647 / NCTC 11838 / VPI 1003)) Explore A4ECA9  Go to UniProtKB:  A4ECA9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.209 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.77	α = 90
b = 83.04	β = 90
c = 47.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Savino, S., Ferrandi, E., Forneris, F., Rovida, S., Riva, S., Monti, D., Mattevi, A.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description