1p4d
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1p4d |SIZE=350|CAPTION= <scene name='initialview01'>1p4d</scene>, resolution 2.60Å | |PDB= 1p4d |SIZE=350|CAPTION= <scene name='initialview01'>1p4d</scene>, resolution 2.60Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= TRAI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= TRAI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4d OCA], [http://www.ebi.ac.uk/pdbsum/1p4d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1p4d RCSB]</span> | ||
}} | }} | ||
| Line 25: | Line 28: | ||
[[Category: Larkin, C.]] | [[Category: Larkin, C.]] | ||
[[Category: Schildbach, J F.]] | [[Category: Schildbach, J F.]] | ||
| - | [[Category: EDO]] | ||
| - | [[Category: MG]] | ||
[[Category: 3 histidine mg(ii) coordination]] | [[Category: 3 histidine mg(ii) coordination]] | ||
[[Category: 5-strand antiparallel beta sheet]] | [[Category: 5-strand antiparallel beta sheet]] | ||
[[Category: alpha-beta]] | [[Category: alpha-beta]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:54:37 2008'' |
Revision as of 19:54, 30 March 2008
| |||||||
| , resolution 2.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | TRAI (Escherichia coli) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
F factor TraI Relaxase Domain
Overview
Conjugative plasmid transfer between bacteria disseminates antibiotic resistance and diversifies prokaryotic genomes. Relaxases, proteins essential for conjugation, cleave one plasmid strand sequence specifically prior to transfer. Cleavage occurs through a Mg(2+)-dependent transesterification involving a tyrosyl hydroxyl and a DNA phosphate. The structure of the F plasmid TraI relaxase domain, described here, is a five-strand beta sheet flanked by alpha helices. The protein resembles replication initiator protein AAV-5 Rep but is circularly permuted, yielding a different topology. The beta sheet forms a binding cleft lined with neutral, nonaromatic residues, unlike most single-stranded DNA binding proteins which use aromatic and charged residues. The cleft contains depressions, suggesting base recognition occurs in a knob-into-hole fashion. Unlike most nucleases, three histidines but no acidic residues coordinate a Mg(2+) located near the catalytic tyrosine. The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage.
About this Structure
1P4D is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structural insights into single-stranded DNA binding and cleavage by F factor TraI., Datta S, Larkin C, Schildbach JF, Structure. 2003 Nov;11(11):1369-79. PMID:14604527
Page seeded by OCA on Sun Mar 30 22:54:37 2008
