Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 18.61 kDa 
• Atom Count: 1266 
• Modelled Residue Count: 153 
• Deposited 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
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.30 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 

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:  
  1MQ7, 1SIX, 1SJN, 1SLH, 1SMC, 1SM8, 1SNF


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	174	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dut, Rv2697c, MT2771, MTCY05A6.18c, MB2716C EC: 3.6.1.23
UniProt
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNS5  Go to UniProtKB:  P9WNS5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP (Subject of Investigation/LOI)	C [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.822	α = 90
b = 54.822	β = 90
c = 84.21	γ = 120

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance