4JE5 | pdb_00004je5

Crystal structure of the aromatic aminotransferase Aro8, a putative alpha-aminoadipate aminotransferase in Saccharomyces cerevisiae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.217 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of Saccharomyces cerevisiae Aro8, a putative alpha-aminoadipate aminotransferase.

Bulfer, S.L., Brunzelle, J.S., Trievel, R.C.

(2013) Protein Sci 22: 1417-1424

  • DOI: https://doi.org/10.1002/pro.2315
  • Primary Citation of Related Structures:  
    4JE5

  • PubMed Abstract: 

    α-Aminoadipate aminotransferase (AAA-AT) catalyzes the amination of 2-oxoadipate to α-aminoadipate in the fourth step of the α-aminoadipate pathway of lysine biosynthesis in fungi. The aromatic aminotransferase Aro8 has recently been identified as an AAA-AT in Saccharomyces cerevisiae. This enzyme displays broad substrate selectivity, utilizing several amino acids and 2-oxo acids as substrates. Here we report the 1.91Å resolution crystal structure of Aro8 and compare it to AAA-AT LysN from Thermus thermophilus and human kynurenine aminotransferase II. Inspection of the active site of Aro8 reveals asymmetric cofactor binding with lysine-pyridoxal-5-phosphate bound within the active site of one subunit in the Aro8 homodimer and pyridoxamine phosphate and a HEPES molecule bound to the other subunit. The HEPES buffer molecule binds within the substrate-binding site of Aro8, yielding insights into the mechanism by which it recognizes multiple substrates and how this recognition differs from other AAA-AT/kynurenine aminotransferases.

    • Organizational Affiliation: 

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic/aminoadipate aminotransferase 1
A, B, C
503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARO8, YGL202W
EC: 2.6.1.39 (PDB Primary Data), 2.6.1.57 (PDB Primary Data)
UniProt
Find proteins for P53090 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53090 
Go to UniProtKB:  P53090
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53090
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic/aminoadipate aminotransferase 1503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARO8, YGL202W
EC: 2.6.1.39 (PDB Primary Data), 2.6.1.57 (PDB Primary Data)
UniProt
Find proteins for P53090 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53090 
Go to UniProtKB:  P53090
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53090
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP
Download Ideal Coordinates CCD File 
I [auth B],
J [auth C]		4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
PLP
Query on PLP
Download Ideal Coordinates CCD File 
E [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
EPE
Query on EPE
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth B],
K [auth C],
L [auth C]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.217 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.442α = 90
b = 159.831β = 106.03
c = 70.642γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PMPClick on this verticalbar to view detailsBest fitted PLPClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2013-10-23
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary