2ZC0 | pdb_00002zc0

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

PDB DOI: https://doi.org/10.2210/pdb2ZC0/pdb

Classification: TRANSFERASE
Organism(s): Thermococcus litoralis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-31 Released: 2008-06-17
Deposition Author(s): Sakuraba, H., Yoneda, K., Tsuge, H., Ohshima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.261 (Depositor), 0.251 (DCC)
R-Value Work:
0.236 (Depositor), 0.238 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of an archaeal alanine:glyoxylate aminotransferase

Sakuraba, H., Yoneda, K., Takeuchi, K., Tsuge, H., Katunuma, N., Ohshima, T.

(2008) Acta Crystallogr D Biol Crystallogr 64: 696-699

PubMed: 18560158 Search on PubMed
DOI: https://doi.org/10.1107/S0907444908006732
Primary Citation Related Structures:
2ZC0

PubMed Abstract:
The crystal structure of a novel alanine:glyoxylate aminotransferase from the hyperthermophilic archaeon Thermococcus litoralis was determined at 2.3 A resolution. The asymmetric unit contains four homologous subunits and the functional tetramer is generated by noncrystallographic 222 symmetry. Although the main-chain coordinates of the monomer of the Thermococcus litoralis enzyme showed a high degree of similarity to those of aspartate aminotransferase from Thermus thermophilus HB8, the amino-acid residues involved in substrate binding in the aspartate aminotransferase are only partially conserved in the Thermococcus litoralis enzyme. This may account for the difference in the substrate specificities of the two enzymes.

Organizational Affiliation

Department of Life System, Institute of Technology and Science, The University of Tokushima, 2-1 Minamijosanjima-cho, Tokushima 770-8506, Japan.

Macromolecule Content

Total Structure Weight: 182.44 kDa
Atom Count: 12,914
Modeled Residue Count: 1,620
Deposited Residue Count: 1,628
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine glyoxylate transaminase	A, B, C, D	407	Thermococcus litoralis	Mutation(s): 0 EC: 2.6.1.44
UniProt
Find proteins for Q9C4M4 (Thermococcus litoralis) Explore Q9C4M4 Go to UniProtKB: Q9C4M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C4M4
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 F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261 (Depositor), 0.251 (DCC)
R-Value Work: 0.236 (Depositor), 0.238 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.694	α = 90
b = 112.519	β = 90
c = 207.287	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2012-04-11
Changes: Database references
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations