4LZB

Uracil binding pocket in Vaccinia virus uracil DNA glycosylase

PDB DOI: https://doi.org/10.2210/pdb4LZB/pdb

Classification: HYDROLASE
Organism(s): Vaccinia virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-07-31 Released: 2013-12-11
Deposition Author(s): Schormann, N., Chattopadhyay, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.246
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the uracil complex of Vaccinia virus uracil DNA glycosylase.

Schormann, N., Banerjee, S., Ricciardi, R., Chattopadhyay, D.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1328-1334

PubMed: 24316823 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309113030613
Primary Citation of Related Structures:
4LZB

PubMed Abstract:
Poxvirus uracil DNA glycosylases are the most diverse members of the family I uracil DNA glycosylases (UNGs). The crystal structure of the uracil complex of Vaccinia virus uracil DNA glycosylase (D4) was determined at 2.03 Å resolution. One uracil molecule was located in the active-site pocket in each of the 12 noncrystallographic symmetry-related D4 subunits. Although the UNGs of the poxviruses (including D4) feature significant differences in the characteristic motifs designated for uracil recognition and in the base-excision mechanism, the architecture of the active-site pocket in D4 is very similar to that in UNGs of other organisms. Overall, the interactions of the bound uracil with the active-site residues are also similar to the interactions previously observed in the structures of human and Escherichia coli UNG.

Organizational Affiliation

Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecule Content

Total Structure Weight: 331.04 kDa
Atom Count: 23,231
Modelled Residue Count: 2,604
Deposited Residue Count: 2,856
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	238	Vaccinia virus	Mutation(s): 1 Gene Names: ACAM3000_MVA_101, D4, MVA101R, UNG EC: 3.2.2.27
UniProt
Find proteins for Q91UM2 (Vaccinia virus (strain Ankara)) Explore Q91UM2 Go to UniProtKB: Q91UM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91UM2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA Query on URA Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain GA [auth C] SDF format, chain IB [auth H] SDF format, chain JA [auth D] SDF format, chain NB [auth I] SDF format, chain OB [auth J] SDF format, chain QA [auth E] SDF format, chain T [auth A] SDF format, chain VA [auth F] SDF format, chain VB [auth L] SDF format, chain FB [auth G] SDF format, chain TB [auth K] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain IB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain NB [auth I] MOL2 format, chain OB [auth J] MOL2 format, chain QA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth L] MOL2 format, chain FB [auth G] MOL2 format, chain TB [auth K]	DA [auth B] FB [auth G] GA [auth C] IB [auth H] JA [auth D] DA [auth B], FB [auth G], GA [auth C], IB [auth H], JA [auth D], NB [auth I], OB [auth J], QA [auth E], T [auth A], TB [auth K], VA [auth F], VB [auth L]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain NB [auth I] Focus chain OB [auth J] Focus chain QA [auth E] Focus chain T [auth A] Focus chain TB [auth K] Focus chain VA [auth F] Focus chain VB [auth L] Interactions & Density Focus chain DA [auth B] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain NB [auth I] Focus chain OB [auth J] Focus chain QA [auth E] Focus chain T [auth A] Focus chain TB [auth K] Focus chain VA [auth F] Focus chain VB [auth L]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain HB [auth H] SDF format, chain KB [auth H] SDF format, chain M [auth A] SDF format, chain PB [auth J] SDF format, chain RA [auth E] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth F] MOL2 format, chain BB [auth G] MOL2 format, chain HB [auth H] MOL2 format, chain KB [auth H] MOL2 format, chain M [auth A] MOL2 format, chain PB [auth J] MOL2 format, chain RA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F]	BB [auth G] HB [auth H] KB [auth H] M [auth A] PB [auth J] BB [auth G], HB [auth H], KB [auth H], M [auth A], PB [auth J], RA [auth E], U [auth B], V [auth B], W [auth B], WA [auth F]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain BB [auth G] Focus chain HB [auth H] Focus chain KB [auth H] Focus chain M [auth A] Focus chain PB [auth J] Focus chain RA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth F] Interactions & Density Focus chain BB [auth G] Focus chain HB [auth H] Focus chain KB [auth H] Focus chain M [auth A] Focus chain PB [auth J] Focus chain RA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DB [auth G] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GB [auth G] SDF format, chain MA [auth D] SDF format, chain MB [auth I] SDF format, chain NA [auth D] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain SB [auth K] SDF format, chain UA [auth E] SDF format, chain UB [auth L] SDF format, chain ZA [auth F] SDF format, chain LB [auth I] SDF format, chain R [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth I] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth K] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth L] MOL2 format, chain ZA [auth F] MOL2 format, chain LB [auth I] MOL2 format, chain R [auth A]	CA [auth B] DB [auth G] EA [auth B] FA [auth B] GB [auth G] CA [auth B], DB [auth G], EA [auth B], FA [auth B], GB [auth G], LB [auth I], MA [auth D], MB [auth I], NA [auth D], Q [auth A], R [auth A], S [auth A], SB [auth K], UA [auth E], UB [auth L], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DB [auth G] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GB [auth G] Focus chain LB [auth I] Focus chain MA [auth D] Focus chain MB [auth I] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth K] Focus chain UA [auth E] Focus chain UB [auth L] Focus chain ZA [auth F] Interactions & Density Focus chain CA [auth B] Focus chain DB [auth G] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GB [auth G] Focus chain LB [auth I] Focus chain MA [auth D] Focus chain MB [auth I] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth K] Focus chain UA [auth E] Focus chain UB [auth L] Focus chain ZA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain HA [auth C] SDF format, chain KA [auth D] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain QB [auth J] SDF format, chain SA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth B] MOL2 format, chain CB [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain QB [auth J] MOL2 format, chain SA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth B]	CB [auth G] HA [auth C] KA [auth D] N [auth A] OA [auth E] CB [auth G], HA [auth C], KA [auth D], N [auth A], OA [auth E], QB [auth J], SA [auth E], X [auth B], XA [auth F], Y [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain HA [auth C] Focus chain KA [auth D] Focus chain N [auth A] Focus chain OA [auth E] Focus chain QB [auth J] Focus chain SA [auth E] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Interactions & Density Focus chain CB [auth G] Focus chain HA [auth C] Focus chain KA [auth D] Focus chain N [auth A] Focus chain OA [auth E] Focus chain QB [auth J] Focus chain SA [auth E] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth G] SDF format, chain BA [auth B] SDF format, chain EB [auth G] SDF format, chain IA [auth C] SDF format, chain JB [auth H] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain RB [auth K] SDF format, chain TA [auth E] SDF format, chain YA [auth F] SDF format, chain LA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth B] MOL2 format, chain EB [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain JB [auth H] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain RB [auth K] MOL2 format, chain TA [auth E] MOL2 format, chain YA [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain Z [auth B]	AA [auth B] AB [auth G] BA [auth B] EB [auth G] IA [auth C] AA [auth B], AB [auth G], BA [auth B], EB [auth G], IA [auth C], JB [auth H], LA [auth D], O [auth A], P [auth A], PA [auth E], RB [auth K], TA [auth E], YA [auth F], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain EB [auth G] Focus chain IA [auth C] Focus chain JB [auth H] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth E] Focus chain RB [auth K] Focus chain TA [auth E] Focus chain YA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain EB [auth G] Focus chain IA [auth C] Focus chain JB [auth H] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth E] Focus chain RB [auth K] Focus chain TA [auth E] Focus chain YA [auth F] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.246
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.47	α = 90
b = 114.045	β = 90
c = 302.516	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
RAPD	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Schormann, N.

Chattopadhyay, D.

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2014-02-05
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description