Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.05 kDa 
• Atom Count: 1289 
• Modelled Residue Count: 155 
• Deposited Residue Count: 163 
• Unique protein chains: 1

1U2Q

Crystal structure of Mycobacterium tuberculosis Low Molecular Weight Protein Tyrosine Phosphatase (MPtpA) at 2.5A resolution with glycerol in the active site

• DOI: 10.2210/pdb1U2Q/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-20 Released: 2005-03-22 
• Deposition Author(s): Madhurantakam, C., Rajakumara, E., Mazumdar, P.A., Saha, B., Mitra, D., Wiker, H.G., Sankaranarayanan, R., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Crystal Structure of Low-Molecular-Weight Protein Tyrosine Phosphatase from Mycobacterium tuberculosis at 1.9-A Resolution

Madhurantakam, C., Rajakumara, E., Mazumdar, P.A., Saha, B., Mitra, D., Wiker, H.G., Sankaranarayanan, R., Das, A.K.

(2005) J Bacteriol 187: 2175-2181

• PubMed: 15743966 
• DOI: 10.1128/JB.187.6.2175-2181.2005
• Primary Citation of Related Structures:  
  1U2P, 1U2Q


• PubMed Abstract: 
  

The low-molecular-weight protein tyrosine phosphatase (LMWPTPase) belongs to a distinctive class of phosphotyrosine phosphatases widely distributed among prokaryotes and eukaryotes. We report here the crystal structure of LMWPTPase of microbial origin, the first of its kind from Mycobacterium tuberculosis. The structure was determined to be two crystal forms at 1.9- and 2.5-A resolutions. These structural forms are compared with those of the LMWPTPases of eukaryotes. Though the overall structure resembles that of the eukaryotic LMWPTPases, there are significant changes around the active site and the protein tyrosine phosphatase (PTP) loop. The variable loop forming the wall of the crevice leading to the active site is conformationally unchanged from that of mammalian LMWPTPase; however, differences are observed in the residues involved, suggesting that they have a role in influencing different substrate specificities. The single amino acid substitution (Leu12Thr [underlined below]) in the consensus sequence of the PTP loop, CTGNICRS, has a major role in the stabilization of the PTP loop, unlike what occurs in mammalian LMWPTPases. A chloride ion and a glycerol molecule were modeled in the active site where the chloride ion interacts in a manner similar to that of phosphate with the main chain nitrogens of the PTP loop. This structural study, in addition to identifying specific mycobacterial features, may also form the basis for exploring the mechanism of the substrate specificities of bacterial LMWPTPases.

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Organizational Affiliation: 

Department of Biotechnology, Indian Institute of Technology, Kharagpur 721 302, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
low molecular weight protein-tyrosine-phosphatase	A	163	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: mptpA EC: 3.1.3.48
UniProt
Find proteins for P9WIA1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIA1  Go to UniProtKB:  P9WIA1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.311	α = 90
b = 53.003	β = 90
c = 64.153	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-20 
• Released Date: 2005-03-22 
Deposition Author(s): Madhurantakam, C., Rajakumara, E., Mazumdar, P.A., Saha, B., Mitra, D., Wiker, H.G., Sankaranarayanan, R., Das, A.K.

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance