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PDBsum entry 1p4d

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1p4d
Jmol
Contents
Protein chains
275 a.a. *
Ligands
EDO ×11
Metals
_MG ×3
Waters ×164
* Residue conservation analysis
PDB id:
1p4d
Name: Hydrolase
Title: F factor trai relaxase domain
Structure: Trai protein. Chain: a, b, c. Fragment: 36 kda n-terminal domain of trai (residues 1-330) synonym: DNA helicase i, contains: trai Protein. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: trai. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.60Å     R-factor:   0.233     R-free:   0.278
Authors: S.Datta,C.Larkin,J.F.Schildbach
Key ref:
S.Datta et al. (2003). Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure, 11, 1369-1379. PubMed id: 14604527 DOI: 10.1016/j.str.2003.10.001
Date:
22-Apr-03     Release date:   14-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14565  (TRAI1_ECOLI) -  Multifunctional conjugation protein TraI
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1756 a.a.
275 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
   Enzyme class 3: E.C.5.99.1.2  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
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.str.2003.10.001 Structure 11:1369-1379 (2003)
PubMed id: 14604527  
 
 
Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
S.Datta, C.Larkin, J.F.Schildbach.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. A Pocket within the Binding Surface of TraI36 Can Accommodate a DNA BaseShown is a model of Gua (shown as sticks) docked into a pocket of TraI36, shown as a molecular surface. The base fits well into the pocket, with little overlap in the van der Waals surfaces of the protein and the base, even without energy minimization of the complex or rearrangement of the protein or base. The surfaces of Arg201 (left) and Gln193 (right) are shown with carbons colored green, nitrogens colored blue, and oxygens colored red. The remainder of the binding pocket is largely hydrophobic. In this orientation, a hydrogen bond can be formed between the Gua O6 and the Arg side chain.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1369-1379) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936510 N.T.Wright, A.Majumdar, and J.F.Schildbach (2011).
Chemical shift assignments for F-plasmid TraI (381-569).
  Biomol NMR Assign, 5, 67-70.  
21439279 R.P.Nash, F.C.Niblock, and M.R.Redinbo (2011).
Tyrosine partners coordinate DNA nicking by the Salmonella typhimurium plasmid pCU1 relaxase enzyme.
  FEBS Lett, 585, 1216-1222.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20890269 A.B.Hickman, J.A.James, O.Barabas, C.Pasternak, B.Ton-Hoang, M.Chandler, S.Sommer, and F.Dyda (2010).
DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans.
  EMBO J, 29, 3840-3852.
PDB codes: 2xm3 2xma 2xo6 2xqc
20435720 L.Dostál, and J.F.Schildbach (2010).
Single-stranded DNA binding by F TraI relaxase and helicase domains is coordinately regulated.
  J Bacteriol, 192, 3620-3628.  
20448025 R.P.Nash, S.Habibi, Y.Cheng, S.A.Lujan, and M.R.Redinbo (2010).
The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1.
  Nucleic Acids Res, 38, 5929-5943.
PDB codes: 3l57 3l6t
19946141 C.E.Alvarez-Martinez, and P.J.Christie (2009).
Biological diversity of prokaryotic type IV secretion systems.
  Microbiol Mol Biol Rev, 73, 775-808.  
19440202 D.R.Boer, J.A.Ruíz-Masó, J.R.López-Blanco, A.G.Blanco, M.Vives-Llàcer, P.Chacón, I.Usón, F.X.Gomis-Rüth, M.Espinosa, O.Llorca, G.del Solar, and M.Coll (2009).
Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.
  EMBO J, 28, 1666-1678.
PDB codes: 3dkx 3dky
19136009 L.M.Guogas, S.A.Kennedy, J.H.Lee, and M.R.Redinbo (2009).
A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer.
  J Mol Biol, 386, 554-568.
PDB code: 3fld
19465049 R.Meyer (2009).
Replication and conjugative mobilization of broad host-range IncQ plasmids.
  Plasmid, 62, 57-70.  
19527679 S.Xia, and J.D.Robertus (2009).
Effect of divalent ions on the minimal relaxase domain of MobA.
  Arch Biochem Biophys, 488, 42-47.  
18250086 A.M.Eldridge, and D.S.Wuttke (2008).
Probing the mechanism of recognition of ssDNA by the Cdc13-DBD.
  Nucleic Acids Res, 36, 1624-1633.  
19152864 B.J.Anderson, C.Larkin, K.Guja, and J.F.Schildbach (2008).
Using fluorophore-labeled oligonucleotides to measure affinities of protein-DNA interactions.
  Methods Enzymol, 450, 253-272.  
18953336 W.Yang (2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
  Nat Struct Mol Biol, 15, 1228-1231.  
17157875 A.F.Monzingo, A.Ozburn, S.Xia, R.J.Meyer, and J.D.Robertus (2007).
The structure of the minimal relaxase domain of MobA at 2.1 A resolution.
  J Mol Biol, 366, 165-178.
PDB code: 2ns6
17660746 B.Gonzalez-Perez, M.Lucas, L.A.Cooke, J.S.Vyle, F.de la Cruz, and G.Moncalián (2007).
Analysis of DNA processing reactions in bacterial conjugation by using suicide oligonucleotides.
  EMBO J, 26, 3847-3857.  
17890221 C.Larkin, R.J.Haft, M.J.Harley, B.Traxler, and J.F.Schildbach (2007).
Roles of active site residues and the HUH motif of the F plasmid TraI relaxase.
  J Biol Chem, 282, 33707-33713.  
17880426 C.Parker, and R.J.Meyer (2007).
The R1162 relaxase/primase contains two, type IV transport signals that require the small plasmid protein MobB.
  Mol Microbiol, 66, 252-261.  
17079132 F.X.Gomis-Rüth, and M.Coll (2006).
Cut and move: protein machinery for DNA processing in bacterial conjugation.
  Curr Opin Struct Biol, 16, 744-752.  
16340015 H.H.Lee, J.Y.Yoon, H.S.Kim, J.Y.Kang, K.H.Kim, D.J.Kim, J.Y.Ha, B.Mikami, H.J.Yoon, and S.W.Suh (2006).
Crystal structure of a metal ion-bound IS200 transposase.
  J Biol Chem, 281, 4261-4266.
PDB codes: 2f4f 2f5g
16923902 R.J.Haft, G.Palacios, T.Nguyen, M.Mally, E.G.Gachelet, E.L.Zechner, and B.Traxler (2006).
General mutagenesis of F plasmid TraI reveals its role in conjugative regulation.
  J Bacteriol, 188, 6346-6353.  
16216584 C.Larkin, S.Datta, M.J.Harley, B.J.Anderson, A.Ebie, V.Hargreaves, and J.F.Schildbach (2005).
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase.
  Structure, 13, 1533-1544.
PDB code: 2a0i
16209952 D.R.Ronning, C.Guynet, B.Ton-Hoang, Z.N.Perez, R.Ghirlando, M.Chandler, and F.Dyda (2005).
Active site sharing and subterminal hairpin recognition in a new class of DNA transposases.
  Mol Cell, 20, 143-154.
PDB codes: 2a6m 2a6o
15028675 H.J.Yeo, and G.Waksman (2004).
Unveiling molecular scaffolds of the type IV secretion system.
  J Bacteriol, 186, 1919-1926.  
15093830 H.Remaut, and G.Waksman (2004).
Structural biology of bacterial pathogenesis.
  Curr Opin Struct Biol, 14, 161-170.  
15123728 J.C.Stern, B.J.Anderson, T.J.Owens, and J.F.Schildbach (2004).
Energetics of the sequence-specific binding of single-stranded DNA by the F factor relaxase domain.
  J Biol Chem, 279, 29155-29159.  
14604517 F.Dyda, and A.B.Hickman (2003).
A mob of reps.
  Structure, 11, 1310-1311.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.