2VE3

Retinoic acid bound cyanobacterial CYP120A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Substrate-Free and Retinoic Acid-Bound Cyanobacterial Cytochrome P450 Cyp120A1.

Kuhnel, K.Ke, N.Cryle, M.J.Sligar, S.G.Schuler, M.A.Schlichting, I.

(2008) Biochemistry 47: 6552

  • DOI: 10.1021/bi800328s
  • Primary Citation of Related Structures:  
    2VE3, 2VE4

  • PubMed Abstract: 
  • The crystal structures of substrate-free and all-trans-retinoic acid-bound CYP120A1 from Synechocystis sp. PCC 6803 were determined at 2.4 and 2.1 A resolution, respectively, representing the first structural characterization of a cyanobacterial P450. Features of CYP120A1 not observed in other P450 structures include an aromatic ladder flanking the channel leading to the active site and a triple-glycine motif within SRS5 ...

    The crystal structures of substrate-free and all-trans-retinoic acid-bound CYP120A1 from Synechocystis sp. PCC 6803 were determined at 2.4 and 2.1 A resolution, respectively, representing the first structural characterization of a cyanobacterial P450. Features of CYP120A1 not observed in other P450 structures include an aromatic ladder flanking the channel leading to the active site and a triple-glycine motif within SRS5. Using spectroscopic methods, CYP120A1 is shown to bind 13-cis-retinoic acid, 9-cis-retinoic acid, and retinal with high affinity and dissociation constants of less than 1 microM. Metabolism of retinoic acid by CYP120A1 suggests that CYP120A1 hydroxylates a variety of retinoid derivatives in vivo. On the basis of the retinoic acid-bound CYP120A1 crystal structure, we propose that either carbon 2 or the methyl groups (C16 or C17) of the beta-ionone ring are modified by CYP120A1.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE CYTOCHROME P450 120A, B444Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.14
UniProt
Find proteins for Q59990 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q59990 
Go to UniProtKB:  Q59990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59990
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
REA
Query on REA

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
REA Binding MOAD:  2VE3 Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.46α = 90
b = 132.97β = 114.5
c = 67.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance