5M8Q

Crystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in complex with kojic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis.

Lai, X.Wichers, H.J.Soler-Lopez, M.Dijkstra, B.W.

(2017) Angew. Chem. Int. Ed. Engl. 56: 9812-9815

  • DOI: 10.1002/anie.201704616
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tyrosinase-related protein 1 (TYRP1) is one of three tyrosinase-like glycoenzymes in human melanocytes that are key to the production of melanin, the compound responsible for the pigmentation of skin, eye, and hair. Difficulties with producing these ...

    Tyrosinase-related protein 1 (TYRP1) is one of three tyrosinase-like glycoenzymes in human melanocytes that are key to the production of melanin, the compound responsible for the pigmentation of skin, eye, and hair. Difficulties with producing these enzymes in pure form have hampered the understanding of their activity and the effect of mutations that cause albinism and pigmentation disorders. Herein we show that the typical tyrosinase-like subdomain of TYRP1 contains two zinc ions in the active site instead of copper ions as found in tyrosinases, which explains why TYRP1 does not exhibit tyrosinase redox activity. In addition, the structures reveal for the first time that the Cys-rich subdomain, which is unique to vertebrate melanogenic proteins, has an epidermal growth factor-like fold and is tightly associated with the tyrosinase subdomain. Our structures suggest that most albinism-related mutations of TYRP1 affect its stability or activity.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5,6-dihydroxyindole-2-carboxylic acid oxidase
A, B, C, D
446Homo sapiensMutation(s): 3 
Gene Names: TYRP1 (CAS2, TYRP, TYRRP)
EC: 1.14.18.-
Find proteins for P17643 (Homo sapiens)
Go to Gene View: TYRP1
Go to UniProtKB:  P17643
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
KOJ
Query on KOJ

Download SDF File 
Download CCD File 
A, B, C, D
5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE
C6 H6 O4
BEJNERDRQOWKJM-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.640α = 90.00
b = 140.426β = 90.00
c = 191.559γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Structure summary