2C27 | pdb_00002c27

The Structure of Mycothiol Synthase in Complex with des- AcetylMycothiol and CoenzymeA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.203 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.161 (Depositor) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

The Substrate-Induced Conformational Change of Mycobacterium Tuberculosis Mycothiol Synthase.

Vetting, M.W.Yu, M.Rendle, P.M.Blanchard, J.S.

(2006) J Biological Chem 281: 2795-2802

  • DOI: https://doi.org/10.1074/jbc.M510798200
  • Primary Citation Related Structures: 
    2C27

  • PubMed Abstract: 

    The structure of the ternary complex of mycothiol synthase from Mycobacterium tuberculosis with bound desacetylmycothiol and CoA was determined to 1.8 A resolution. The structure of the acetyl-CoA-binary complex had shown an active site groove that was several times larger than its substrate. The structure of the ternary complex reveals that mycothiol synthase undergoes a large conformational change in which the two acetyltransferase domains are brought together through shared interactions with the functional groups of desacetylmycothiol, thereby decreasing the size of this large central groove. A comparison of the binary and ternary structures illustrates many of the features that promote catalysis. Desacetylmycothiol is positioned with its primary amine in close proximity and in the proper orientation for direct nucleophilic attack on the si-face of the acetyl group of acetyl-CoA. Glu-234 and Tyr-294 are positioned to act as a general base and general acid to promote acetyl transfer. In addition, this structure provides further evidence that the N-terminal acetyltransferase domain no longer has enzymatic activity and is vestigial in nature.


  • Organizational Affiliation
    • Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461-1602, USA.

Macromolecule Content 

  • Total Structure Weight: 35.66 kDa 
  • Atom Count: 2,555 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MYCOTHIOL SYNTHASE315Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 2.3.1.189
UniProt
Find proteins for P9WJM7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJM7 
Go to UniProtKB:  P9WJM7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJM7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO

Query on ACO



Download:Ideal Coordinates CCD File
C [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
COA

Query on COA



Download:Ideal Coordinates CCD File
D [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MA8

Query on MA8



Download:Ideal Coordinates CCD File
B [auth A](1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside
C15 H28 N2 O11 S
ZGXSCMBZZVXWGF-BSEFFJTHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.203 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.161 (Depositor) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.83α = 90
b = 59.62β = 91.57
c = 61.67γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-01
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary