4ATQ | pdb_00004atq

GABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct

PDB DOI: https://doi.org/10.2210/pdb4ATQ/pdb

Classification: TRANSFERASE
Organism(s): Paenarthrobacter aurescens TC1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-09 Released: 2012-10-10
Deposition Author(s): Bruce, H., Tuan, A.N., Mangas Sanchez, J., Hart, S., Turkenburg, J.P., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.248 (Depositor), 0.243 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structures of a Gamma-Aminobutyrate (Gaba) Transaminase from the S-Triazine-Degrading Organism Arthrobacter Aurescens Tc1 in Complex with Plp and with its External Aldimine Plp- Gaba Adduct.

Bruce, H., Nguyen Tuan, A., Mangas Sanchez, J., Leese, C., Hopwood, J., Hyde, R., Hart, S., Turkenburg, J.P., Grogan, G.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1175

PubMed: 23027742 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309112030023
Primary Citation Related Structures:
4ATP, 4ATQ

PubMed Abstract:
Two complex structures of the γ-aminobutyrate (GABA) transaminase A1R958 from Arthrobacter aurescens TC1 are presented. The first, determined to a resolution of 2.80 Å, features the internal aldimine formed by reaction between the ℇ-amino group of Lys295 and the cofactor pyridoxal phosphate (PLP); the second, determined to a resolution of 2.75 Å, features the external aldimine adduct formed between PLP and GABA in the first half-reaction. This is the first structure of a microbial GABA transaminase in complex with its natural external aldimine and reveals the molecular determinants of GABA binding in this enzyme.

Organizational Affiliation

York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England.

Macromolecule Content

Total Structure Weight: 575.81 kDa
Atom Count: 38,709
Modeled Residue Count: 5,284
Deposited Residue Count: 5,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-AMINOBUTYRATE TRANSAMINASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	456	Paenarthrobacter aurescens TC1	Mutation(s): 0 EC: 2.6.1.19 (PDB Primary Data), 2.6.1.22 (UniProt)
UniProt
Find proteins for A1R958 (Paenarthrobacter aurescens (strain TC1)) Explore A1R958 Go to UniProtKB: A1R958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1R958
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 Y [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
ABU Query on ABU Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.248 (Depositor), 0.243 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.71	α = 90
b = 292.83	β = 90
c = 105.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-10-17
Changes: Database references
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Other
Version 2.1: 2023-12-20
Changes: Refinement description