1ZYU | pdb_00001zyu

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate and amppcp at 2.85 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.251 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of Mycobacterium tuberculosis Shikimate Kinase in Complex with Shikimic Acid and an ATP Analogue

Gan, J.H.Gu, Y.J.Li, Y.Yan, H.G.Ji, X.

(2006) Biochemistry 45: 8539-8545

  • DOI: https://doi.org/10.1021/bi0606290
  • Primary Citation Related Structures: 
    1ZYU, 2G1J, 2G1K

  • PubMed Abstract: 

    Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs, because the pathway is essential in microorganisms, plants, and parasites but absent from mammals. SK catalyzes the reaction of phosphoryl transfer from ATP to shikimic acid (SA). Since 2002, a total of 11 SK structures have been reported, but none contains either the two substrate (SA and ATP) or the two product (SA-phosphate and ADP) molecules. Here, we present three crystal structures of SK from Mycobacterium tuberculosis (MtSK), including apo-MtSK, a binary complex MtSK x SA, and the ternary complex of MtSK with SA and an ATP analogue, AMPPCP. The structures of apo-MtSK and MtSK x AMPPCP x SA make it possible to elucidate the conformational changes of MtSK upon the binding of both substrates; the structure of MtSK x AMPPCP x SA reveals interactions between the protein and gamma-phosphate which indicate dynamic roles of catalytic residues Lys15 and Arg117.


  • Organizational Affiliation
    • Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.

Macromolecule Content 

  • Total Structure Weight: 19.29 kDa 
  • Atom Count: 1,343 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 176 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Shikimate kinase176Mycobacterium tuberculosisMutation(s): 0 
Gene Names: aroK
EC: 2.7.1.71
UniProt
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY3 
Go to UniProtKB:  P9WPY3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPY3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP

Query on ACP



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
SKM

Query on SKM



Download:Ideal Coordinates CCD File
C [auth A](3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.251 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.954α = 90
b = 59.954β = 90
c = 102.666γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Database references, Structure summary