PDBsum entry 3fld

Hydrolase

PDB id: 3fld

Contents

Protein chains

152 a.a. *

Ligands

SO4 ×10

Waters ×130

* Residue conservation analysis

PDB id:

3fld

Name:

Hydrolase

Title:

Crystal structure of the trai c-terminal domain

Structure:

Protein trai. Chain: a, b. Fragment: unp residues 1476-1628. Synonym: DNA helicase i. Engineered: yes

Source:

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. Gene: ecok12f104, trai. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.220 R-free: 0.263

Authors:

L.M.Guogas,S.A.Kennedy,M.R.Redinbo

Key ref:

L.M.Guogas et al. (2009). A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer. J Mol Biol, 386, 554-568. PubMed id: 19136009 DOI: 10.1016/j.jmb.2008.12.057

Date:

18-Dec-08 Release date: 10-Feb-09

Protein chains

P14565  (TRAI1_ECOLI) -  Multifunctional conjugation protein TraI from Escherichia coli (strain K12)

Seq: 1756 a.a.

Struc: 152 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 3: E.C.5.6.2.1 - Dna topoisomerase.

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.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2008.12.057

J Mol Biol 386:554-568 (2009)

PubMed id: 19136009

A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer.

L.M.Guogas, S.A.Kennedy, J.H.Lee, M.R.Redinbo.

ABSTRACT

TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-A resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal alpha-domain connected by a proline-rich loop to a compact alpha/beta-domain. Both the globular nature of the alpha/beta-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.

Selected figure(s)

Figure 6.
Fig. 6. (a) CDT efficiencies of E. coli strains containing specifically designed TraI-CT mutations. (b) “pmut” indicates the mutation of prolines 1518, 1523, and 1525 simultaneously to glycine, while “Δloop” indicates the removal of the entire proline-rich loop. (c) The h1/s1 variant is the mutations of V1478, E1482, and F1485 to alanine on helix 1 and the mutation of I1541 to alanine and that of G1540 to glutamic acid on strand 2. (Helix 1 is shown here in orange to indicate the domain-swapped interaction.) (d) The h3/s2 (helix 3/sheet 2) mutants replace L1574, Q1575, and V1603 all with alanine.

Figure 7.
Fig. 7. Binding of ssDNA by the TraI-CT measured by fluorescence anisotropy. TraI 1476–1756 at 75 and 150 mM NaCl is indicated by continuous and dashed blue lines (K[d] = 2.9 μM and K[d] = 7.7 μM), respectively. TraI 1476–1756 with a deletion of the proline-rich loop at 75 and 150 mM NaCl is indicated by continuous and dashed red lines (K[d] > 17.1 μM and K[d] > 15.9 μM), respectively. TraI 1476–1756 with mutations of prolines 1518, 1523, and 1525 to glycine at 75 and 150 mM NaCl is indicated by continuous and dashed green lines (K[d] > 13.9 μM and K[d] > 18.2 μM), respectively, while the binding of 1476–1630 at 150 mM NaCl is indicated in black (K[d] > 22.6 μM).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 386, 554-568) copyright 2009.

Figures were selected by an automated process.