1GC4 | pdb_00001gc4

THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH ASPARTATE

PDB DOI: https://doi.org/10.2210/pdb1GC4/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-07-19 Released: 2001-09-05
Deposition Author(s): Ura, H., Nakai, T., Hirotsu, K., Kuramitsu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.277 (Depositor), 0.264 (DCC)
R-Value Work:
0.217 (Depositor), 0.206 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Substrate recognition mechanism of thermophilic dual-substrate enzyme.

Ura, H., Nakai, T., Kawaguchi, S.I., Miyahara, I., Hirotsu, K., Kuramitsu, S.

(2001) J Biochem 130: 89-98

PubMed: 11432784 Search on PubMed
DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002966
Primary Citation Related Structures:
1B5O, 1B5P, 1GC3, 1GC4, 1GCK, 5BJ3, 5BJ4

PubMed Abstract:
Aspartate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus HB8 (ttAspAT), has been believed to be specific for an acidic substrate. However, stepwise introduction of mutations in the active-site residues finally changed its substrate specificity to that of a dual-substrate enzyme. The final mutant, [S15D, T17V, K109S, S292R] ttAspAT, is active toward both acidic and hydrophobic substrates. During the course of stepwise mutation, the activities toward acidic and hydrophobic substrates changed independently. The introduction of a mobile Arg292* residue into ttAspAT was the key step in the change to a "dual-substrate" enzyme. The substrate recognition mechanism of this thermostable "dual-substrate" enzyme was confirmed by X-ray crystallography. This work together with previous studies on various enzymes suggest that this unique "dual-substrate recognition" mechanism is a feature of not only aminotransferases but also other enzymes.

Organizational Affiliation

Department of Biology, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

Macromolecule Content

Total Structure Weight: 170.15 kDa
Atom Count: 11,888
Modeled Residue Count: 1,528
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE AMINOTRANSFERASE	A, B, C, D	385	Thermus thermophilus HB8	Mutation(s): 4 EC: 2.6.1.1 (PDB Primary Data), 2.6.1.78 (UniProt)
UniProt
Find proteins for Q56232 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56232 Go to UniProtKB: Q56232
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56232
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 L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.277 (Depositor), 0.264 (DCC)
R-Value Work: 0.217 (Depositor), 0.206 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.67	α = 90
b = 102.34	β = 112.14
c = 100.41	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2001-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-09-05
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2019-10-16
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2019-12-04
Changes: Derived calculations
Version 1.5: 2021-11-10
Changes: Database references, Derived calculations
Version 1.6: 2023-12-27
Changes: Data collection