2ZP7

Crystal structure of LysN, alpha-aminoadipate aminotransferase (Leucine complex), from Thermus thermophilus HB27

PDB DOI: https://doi.org/10.2210/pdb2ZP7/pdb
Entry: 2ZP7 supersedes: 2ZG5

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-30 Released: 2009-01-13
Deposition Author(s): Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.263
R-Value Work: 0.205
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus

Tomita, T., Miyagawa, T., Miyazaki, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

(2008) Proteins

PubMed: 18831049 Search on PubMed
DOI: https://doi.org/10.1002/prot.22245
Primary Citation of Related Structures:
2ZP7, 3CBF

PubMed Abstract:
Alpha-aminoadipate aminotransferase (AAA-AT), a homolog of mammalian kynurenine aminotransferase II (Kat II), transfers an amino group to 2-oxoadipate to yield alpha-aminoadipate in lysine biosynthesis through the alpha-aminoadipate pathway in Thermus thermophilus. AAA-AT catalyzes transamination against various substrates, including AAA, glutamate, leucine, and aromatic amino acids. To elucidate the structural change for recognition of various substrates, we determined crystal structures of AAA-AT in four forms: with pyridoxal 5'-phosphate (PLP) (PLP complex), with PLP and leucine (PLP/Leu complex), with N-phosphopyridoxyl-leucine (PPL) (PPL complex), and with N-phosphopyridoxyl-alpha-aminoadipate (PPA) at 2.67, 2.26, 1.75, and 1.67 A resolution, respectively. The PLP complex is in an open state, whereas PLP/Leu, PPL, and PPA complexes are in closed states with maximal displacement (over 7 A) of the alpha2 helix and the beta1 strand in the small domain to cover the active site, indicating that conformational change is induced by substrate binding. In PPL and PLP/Leu complexes, several hydrophobic residues on the alpha2 helix recognize the hydrophobic side chain of the bound leucine moiety whereas, in the PPA complex, the alpha2 helix rotates to place the guanidium moiety of Arg23 on the helix at the appropriate position to interact with the carboxyl side chain of the AAA moiety. These results indicate that AAA-AT can recognize various kinds of substrates using the mobile alpha2 helix. The crystal structures and site-directed mutagenesis revealed that intersubunit-electrostatic interactions contribute to the elevated thermostability of this enzyme.

Organizational Affiliation

Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 265.27 kDa
Atom Count: 18,870
Modelled Residue Count: 2,346
Deposited Residue Count: 2,382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-aminodipate aminotransferase	A, B, C, D, E A, B, C, D, E, F	397	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: lysN EC: 2.6.1.39
UniProt
Find proteins for Q72LL6 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72LL6 Go to UniProtKB: Q72LL6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72LL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain O [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F]	G [auth A] I [auth B] K [auth C] L [auth D] M [auth E] G [auth A], I [auth B], K [auth C], L [auth D], M [auth E], O [auth F]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F]
LEU Query on LEU Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain N [auth E] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth E]	H [auth A], J [auth B], N [auth E]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth E]