PDBsum entry: 1cy6

Isomerase

PDB-id: 1cy6

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Description

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Header records

References

PROCHECK

Protein chain

562 a.a. *

Ligands

PO4 ×3

T3P

Waters ×109

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1cy6

Name:

Isomerase

Title:

Complex of e.Coli DNA topoisomerase i with 3' thymidine monophosphate

Structure:

DNA topoisomerase i. Chain: a. Fragment: 67 kda n-terminal fragment of e.Coli topoisomerase i. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

P06612 (TOP1_ECOLI)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

865 a.a.

Struc:

562 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.5.99.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

Resolution:

2.50Å

R-factor:

0.244

R-free:

0.309

Authors:

H.Feinberg,A.Changela,A.Mondragon

Key ref:

H.Feinberg et al. (1999). Protein-nucleotide interactions in E. coli DNA topoisomerase I.. Nat Struct Biol, 6, 961-968. [PubMed id: 10504732] [DOI: 10.1038/13333]

Date:

31-Aug-99

Release date:

08-Mar-00

Related entries:

1cy0
complex of e.Coli DNA topoisomerase i with 3'-5'-adenosine
diphosphate
1cy1
complex of e.Coli DNA topoisomerase i with 5'ptptpt
1cy4
complex of e.Coli DNA topoisomerase i with 5'ptptptp3'
1cy2
complex of e.Coli DNA topoisomerase i with tptptp3'
1cy7
... plus others (see Header records)

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Clefts

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Key reference

DOI no: 10.1038/13333

Nat Struct Biol 6:961-968 (1999)

PubMed id: 10504732

Protein-nucleotide interactions in E. coli DNA topoisomerase I.

H.Feinberg, A.Changela, A.Mondragón.

ABSTRACT

DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.

Selected figure(s)

Figure 3.
Figure 3. Models showing different conformations of the loop region in domain III. a, Overall view illustrating three different conformations of a loop consisting of residues 357−364 located near the active site. The green model represents the structure of the 3'5'ADP complex showing an ordered loop in a closed conformation. A structure of the 30 kDa fragment of E. coli DNA topoisomerase I^10, which contains an ordered loop, is shown in red. The loop in this model of the 30 kDa fragment is in an open conformation. The structure of the 5'pTTT complex is in blue. The loop is mostly disordered in the 5'pTTT model although two ordered residues (Glu 363 and Ala 364) can be seen. This structure of this loop seems to be in between the open and the closed conformations. The structures of domain III from all three models were superimposed in this panel. b, A stereo closeup view of the loop region. The model of the 5'pTTT complex is in blue, the 3'5'ADP model is in green, and the 30 kDa fragment is colored red. The different orientations of His 365 with respect to the nucleotide in site I can be seen. In the open conformation, represented by the structure of the 30 kDa fragment, His 365 points towards the nucleotide in site I. In the closed conformation depicted by the 3'5'ADP model, His 365 points away from the nucleotide. In the model of the 5'pTTT complex, His 365 is directed towards the nucleotide. Drawings were prepared using MOLSCRIPT^30.

Figure 4.
Figure 4. Stereo view of the active site region. The model of the 5'pT complex shows the location of the nucleotide at site I with respect to the active site region. Conserved residues in the active site region are labeled; hydrogen bonds and salt bridges are shown as dotted lines. The 5'pT molecule makes contacts with Arg 114 and Arg 161. The extensive hydrogen bond network found in the interface between domains I and III is also illustrated. Tyr 319 contacts Asp 111 through a water molecule, which also contacts Glu 115 . Arg 321 makes salt bridges to both Asp 113 and Glu 115. Clearly, a single stranded DNA molecule could bind in the same site and extend to the active site if the protein is in the open conformation. Site I appears to be one or two nucleotides away from the active site. The drawing was prepared using MOLSCRIPT^30 and RASTER3D^32, ^33.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 961-968) copyright 1999.

Figures were selected by an automated process.