	233,605 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

4WRY|pdb_00004wry

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-fluorouracil(B), Form I

PDB DOI: https://doi.org/10.2210/pdb4WRY/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-25 Released: 2015-07-15
Deposition Author(s): Arif, S.M.,Geethanandan, K.,Mishra, P.,Surolia, A.,Varshney, U.,Vijayan, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.158 (Depositor), 0.160 (DCC)
R-Value Work:
0.108 (Depositor), 0.110 (DCC)
R-Value Observed:
0.111 (Depositor)

Starting Model:experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications.

Arif, S.M., Geethanandan, K., Mishra, P., Surolia, A., Varshney, U., Vijayan, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1514-1527

PubMed: 26143923 Search on PubMed
DOI: https://doi.org/10.1107/S1399004715009311
Primary Citation of Related Structures:
4WPK,4WPL,4WRU,4WRV,4WRW,4WRX,4WRY,4WRZ,4WS0,4WS1,4WS2,4WS3,4WS4,4WS5,4WS6,4WS7,4WS8

PubMed Abstract:
17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5' position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecule Content

Total Structure Weight: 26.17 kDa
Atom Count: 2,045
Modelled Residue Count: 225
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	238	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ung, Rv2976c, MTCY349.11 EC: 3.2.2.27
UniProt
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFQ9 Go to UniProtKB: P9WFQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
URF Query on URF Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-FLUOROURACIL C₄ H₃ F N₂ O₂ GHASVSINZRGABV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.158 (Depositor), 0.160 (DCC)
R-Value Work: 0.108 (Depositor), 0.110 (DCC)
R-Value Observed: 0.111 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.99	α = 90
b = 63.39	β = 114.06
c = 45.23	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-15
Type: Initial release
Version 1.1: 2015-07-22
Changes: Database references
Version 1.2: 2017-11-22
Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description