Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 18605.92 
• Atom Count: 1148 
• Residue Count: 174 
• Unique protein chains: 1

1SIX

Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP

• DOI: 10.2210/pdb1SIX/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli


• Deposited: 2004-03-01 Released: 2004-03-09 
• Deposition Author(s): Sawaya, M.R., Chan, S., Segelke, B., Lekin, T., Krupka, H., Cho, U.-S., Kim, M., So, M., Kim, C.-Y., Naranjo, C.M., Rogers, Y.C., Park, M.S., Waldo, G.S., Pashkov, I., Cascio, D., Yeates, T.O., Perry, J.L., Terwilliger, T.C., Eisenberg, D., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 

Literature

Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.

Chan, S., Segelke, B., Lekin, T., Krupka, H., Cho, U.S., Kim, M.-Y., So, M., Kim, C.-Y., Naranjo, C.M., Rogers, Y.C., Park, M.S., Waldo, G.S., Pashkov, I., Cascio, D., Perry, J.L., Sawaya, M.R.

(2004) J.Mol.Biol. 341: 503-517

• PubMed: 15276840 
• DOI: 10.1016/j.jmb.2004.06.028
• Primary Citation of Related Structures:  
  1SNF, 1SMC, 1SM8, 1SLH, 1SJN, 1MQ7


• PubMed Abstract: 
  

The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.

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Organizational Affiliation: 

UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 206 Boyer Hall, Box 951570, Los Angeles, CA 90095-1570, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	174	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mutation(s): 0  Gene Names: dut EC: 3.6.1.23
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WNS5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DUP	A	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRIS BUFFER C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 54.822	α = 90.00
b = 54.822	β = 90.00
c = 84.210	γ = 120.00

Software Package:

Software Name	Purpose
SHELX	model building
EPMR	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-01 
• Released Date: 2004-03-09 
• Deposition Author(s): Sawaya, M.R., Chan, S., Segelke, B., Lekin, T., Krupka, H., Cho, U.-S., Kim, M., So, M., Kim, C.-Y., Naranjo, C.M., Rogers, Y.C., Park, M.S., Waldo, G.S., Pashkov, I., Cascio, D., Yeates, T.O., Perry, J.L., Terwilliger, T.C., Eisenberg, D., TB Structural Genomics Consortium (TBSGC)

Revision History 

• Version 1.0: 2004-03-09
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance