PDBsum entry 1lqm

Hydrolase/hydrolase inhibitor

PDB id: 1lqm

Contents

Protein chains

223 a.a. *

82 a.a. *

Waters ×58

* Residue conservation analysis

PDB id:

1lqm

Name:

Hydrolase/hydrolase inhibitor

Title:

Escherichia coli uracil-DNA glycosylase complex with uracil-DNA glycosylase inhibitor protein

Structure:

Uracil-DNA glycosylase. Chain: a, c, e, g. Synonym: udg. Uracil-DNA-glycosylase. Engineered: yes. Uracil-DNA glycosylase inhibitor. Chain: b, d, f, h. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Bacillus phage pbs2. Organism_taxid: 10684. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.20Å R-factor: 0.188 R-free: 0.260

Authors:

K.Saikrishnan,M.B.Sagar,R.Ravishankar,S.Roy,K.Purnapatre,U.Varshney, M.Vijayan

Key ref:

K.Saikrishnan et al. (2002). Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG. Acta Crystallogr D Biol Crystallogr, 58, 1269-1276. PubMed id: 12136137 DOI: 10.1107/S0907444902009599

Date:

10-May-02 Release date: 10-Nov-02

Protein chains

P12295  (UNG_ECOLI) -  Uracil-DNA glycosylase from Escherichia coli (strain K12)

Seq: 229 a.a.

Struc: 223 a.a.

Protein chains

P14739  (UNGI_BPPB2) -  Uracil-DNA glycosylase inhibitor from Bacillus phage PBS2

Seq: 84 a.a.

Struc: 82 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, C, E, G: E.C.3.2.2.27 - uracil-DNA glycosylase.
• Enzyme class 3: Chains B, D, F, H: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1107/S0907444902009599

Acta Crystallogr D Biol Crystallogr 58:1269-1276 (2002)

PubMed id: 12136137

Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.

K.Saikrishnan, M.Bidya Sagar, R.Ravishankar, S.Roy, K.Purnapatre, P.Handa, U.Varshney, M.Vijayan.

ABSTRACT

The structures of a new crystal form of free Escherichia coli uracil DNA glycosylase (UDG), containing four molecules in the asymmetric unit, and two forms of its complex with the proteinaceous inhibitor Ugi, containing two and four crystallographically independent complexes, have been determined. A comparison of these structures and the already known crystal structures containing UDG shows that the enzyme can be considered to be made up of two independently moving structural entities or domains. A detailed study of free and DNA-bound human enzyme strengthens this conclusion. The domains close upon binding to uracil-containing DNA, whereas they do not appear to do so upon binding to Ugi. The comparative study also shows that the mobility of the molecule involves the rigid-body movement of the domains superposed on flexibility within domains.

Selected figure(s)

Figure 3.
Figure 3 Delineation of domains in EcUDG. Domain 1 is in green and domain 2 is in red. The linker region is in purple. The axis about which the domains move during closure is also shown.

Figure 4.
Figure 4 Stereoview illustrating domain closure in EcUDG. Domain 1 of the free enzyme (dark) and that of the enzyme complexed with single-stranded DNA (light) are superposed. The axis about which the molecule has to rotate to bring domain 2 into superposition is perpendicular to the figure and is indicated by a ball.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1269-1276) copyright 2002.

Figures were selected by an automated process.