6HNV | pdb_00006hnv

Crystal structure of aminotransferase Aro9 from C. Albicans with ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HNV

Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

Literature

Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties.

Kiliszek, A.Rypniewski, W.Rzad, K.Milewski, S.Gabriel, I.

(2019) J Struct Biol 205: 26-33

  • DOI: https://doi.org/10.1016/j.jsb.2019.02.001
  • Primary Citation Related Structures: 
    6HNB, 6HND, 6HNU, 6HNV

  • PubMed Abstract: 

    Aminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5'-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting different catalytic properties. To elucidate the multiple substrate recognition of the two enzymes we determined the crystal structures of an unliganded CaAro8p, a complex of CaAro8p with the PLP cofactor bound to a substrate, forming an external aldimine, CaAro9p with PLP in the form of internal aldimine, and CaAro9p with a mixture of ligands that have been interpreted as results of the enzymatic reaction. The crystal structures of both enzymes contains in the asymmetric unit a biologically relevant dimer of 55 kDa for CaAro8 and 59 kDa for CaAro9p protein subunits. The ability of the enzymes to process multiple substrates could be related to a feature of their architecture in which the active site resides on one subunit while the substrate-binding site is formed by a long loop extending from the other subunit of the dimeric molecule. The separation of the two functions to different chemical entities could facilitate the evolution of the substrate-binding part and allow it to be flexible without destabilizing the conservative catalytic mechanism.


  • Organizational Affiliation
    • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland.

Macromolecule Content 

  • Total Structure Weight: 119.8 kDa 
  • Atom Count: 7,849 
  • Modeled Residue Count: 934 
  • Deposited Residue Count: 1,048 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aromatic-amino-acid:2-oxoglutarate transaminase
A, B
524Candida albicansMutation(s): 0 
Gene Names: ARO9orf19.1237CAALFM_C405560CA
UniProt
Find proteins for A0A1D8PMC5 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PMC5 
Go to UniProtKB:  A0A1D8PMC5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8PMC5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PHE

Query on PHE



Download:Ideal Coordinates CCD File
F [auth A]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
PPY

Query on PPY



Download:Ideal Coordinates CCD File
G [auth A]3-PHENYLPYRUVIC ACID
C9 H8 O3
BTNMPGBKDVTSJY-UHFFFAOYSA-N
BCN

Query on BCN



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B],
K [auth B]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
UN1

Query on UN1



Download:Ideal Coordinates CCD File
I [auth B]2-AMINOHEXANEDIOIC ACID
C6 H11 N O4
OYIFNHCXNCRBQI-BYPYZUCNSA-N
OOG

Query on OOG



Download:Ideal Coordinates CCD File
L [auth B]2-OXOADIPIC ACID
C6 H8 O5
FGSBNBBHOZHUBO-UHFFFAOYSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.57α = 90
b = 88.54β = 90
c = 160.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
2015/17/B/NZ6/04248

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 2.0: 2019-03-06
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references