4JE5 | pdb_00004je5

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

PDB DOI: https://doi.org/10.2210/pdb4JE5/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-26 Released: 2013-09-11
Deposition Author(s): Bulfer, S.L., Brunzelle, J.S., Trievel, R.C.

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)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 23893908 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.2315
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 228.43 kDa
Atom Count: 16,855
Modeled Residue Count: 1,979
Deposited Residue Count: 2,012
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic/aminoadipate aminotransferase 1	A, B, C	503	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53090
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic/aminoadipate aminotransferase 1	D	503	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53090
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B]	I [auth B], J [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth C]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

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 = 227.442	α = 90
b = 159.831	β = 106.03
c = 70.642	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Bulfer, S.L.

Brunzelle, J.S.

Trievel, R.C.

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