1FK8 | pdb_00001fk8

THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX WITH NAD OF 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE FROM COMAMONAS TESTOSTERONI, A MEMBER OF THE SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY

• PDB DOI: https://doi.org/10.2210/pdb1FK8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Comamonas testosteroni
• Mutation(s): No 


• Deposited: 2000-08-09 Released: 2001-01-17 
• Deposition Author(s): Grimm, C., Ficner, R., Maser, E., Klebe, G., Reuter, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.220 (Depositor) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family.

Grimm, C., Maser, E., Mobus, E., Klebe, G., Reuter, K., Ficner, R.

(2000) J Biological Chem 275: 41333-41339

• PubMed: 11007791 
• DOI: https://doi.org/10.1074/jbc.M007559200
• Primary Citation Related Structures: 
  1FJH, 1FK8


• PubMed Abstract: 
  

  The crystal structure of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni (3alpha-HSDH) as well as the structure of its binary complex with NAD(+) have been solved at 1.68-A and 1.95-A resolution, respectively. The enzyme is a member of the short chain dehydrogenase/reductase (SDR) family. Accordingly, the active center and the conformation of the bound nucleotide cofactor closely resemble those of other SDRs. The crystal structure reveals one homodimer per asymmetric unit representing the physiologically active unity. Dimerization takes place via an interface essentially built-up by helix alphaG and strand betaG of each subunit. So far this type of intermolecular contact has exclusively been observed in homotetrameric SDRs but never in the structure of a homodimeric SDR. The formation of a tetramer is blocked in 3alpha-HSDH by the presence of a predominantly alpha-helical subdomain which is missing in all other SDRs of known structure.

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Organizational Affiliation: 
• Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, 35037 Marburg, Germany.

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: 54.17 kDa 
• Atom Count: 3,858 
• Modeled Residue Count: 476 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE	A, B	257	Comamonas testosteroni	Mutation(s): 0  EC: 1.1.1.50
UniProt
Find proteins for P80702 (Comamonas testosteroni) Explore P80702  Go to UniProtKB:  P80702

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.220 (Depositor) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.785	α = 107.52
b = 46.195	β = 106.34
c = 64.982	γ = 97.63

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-17 
Deposition Author(s): Grimm, C., Ficner, R., Maser, E., Klebe, G., Reuter, K.

Revision History  

• Version 1.0: 2001-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations