1J4J | pdb_00001j4j

Crystal Structure of Tabtoxin Resistance Protein (form II) complexed with an Acyl Coenzyme A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.254 (Depositor) 
  • R-Value Work: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation.

He, H., Ding, Y., Bartlam, M., Sun, F., Le, Y., Qin, X., Tang, H., Zhang, R., Joachimiak, A., Liu, J., Zhao, N., Rao, Z.

(2003) J Mol Biology 325: 1019-1030

  • DOI: https://doi.org/10.1016/s0022-2836(02)01284-6
  • Primary Citation Related Structures: 
    1GHE, 1J4J

  • PubMed Abstract: 

    Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55A resolution. The binary complex forms a characteristic "V" shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

    • Organizational Affiliation: 
    • Laboratory of Structural Biology, and MOE Laboratory of Protein Science, School of Life Sciences and Engineering, Tsinghua University, 100084, Beijing, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 40.51 kDa 
  • Atom Count: 2,879 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 354 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TABTOXIN RESISTANCE PROTEIN
A, B
177Pseudomonas amygdali pv. tabaciMutation(s): 4 
EC: 2.3.1
UniProt
Find proteins for P16966 (Pseudomonas amygdali pv. tabaci)
Explore P16966 
Go to UniProtKB:  P16966
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16966
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO

Query on ACO


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.254 (Depositor) 
  • R-Value Work:  0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.667α = 90
b = 66.593β = 103.682
c = 53.599γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
Omodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Structure summary