3k70

From Proteopedia

(Difference between revisions)

Revision as of 05:44, 9 February 2016

Crystal structure of the complete initiation complex of RecBCD

Structural highlights

3k70 is a 8 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1w36
Gene:	b2820, JW2788, recB, rorA (ECOLI), b2822, JW2790, recC (ECOLI), b2819, JW2787, recD (ECOLI)
Activity:	Exodeoxyribonuclease V, with EC number 3.1.11.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[EX5B_ECOLI] Required for efficient DNA repair; it catalyzes the unwinding of double-stranded DNA and the cleavage of single-stranded DNA and it stimulates local genetic recombination. All of these activities require concomitant hydrolysis of ATP. [EX5A_ECOLI] Exhibits several catalytic activities, including ATP-dependent exonuclease, ATP-stimulated endonuclease, ATP-dependent unwinding and DNA-dependent ATPase activities. Strand cleavage occurs 5' to 3' during the unwinding of duplex DNA at CHI sequences, which locally stimulate recombination. [EX5C_ECOLI] Exhibits a wide variety of catalytic activities including ATP-dependent exonuclease, ATP-stimulated endonuclease, ATP-dependent helicase and DNA-dependent ATPase activities.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The molecular mechanism of superfamily 1Balpha helicases remains unclear. We present here the crystal structure of the RecD2 helicase from Deinococcus radiodurans at 2.2-A resolution. The structure reveals the folds of the 1B and 2B domains of RecD that were poorly ordered in the structure of the Escherichia coli RecBCD enzyme complex reported previously. The 2B domain adopts an SH3 fold which, although common in eukaryotes, is extremely rare in bacterial systems. In addition, the D. radiodurans RecD2 structure has aided us in deciphering lower resolution (3.6 A) electron density maps for the E. coli RecBCD enzyme in complex with a long DNA substrate that interacts with the RecD subunit. Taken together, these structures indicated an important role for the 1B domain of RecD, a beta-hairpin that extends from the surface of the 1A domain and interacts with the DNA substrate. On the basis of these structural data, we designed a mutant RecD2 helicase that lacks this pin. The 'pin-less' mutant protein is a fully active ssDNA-dependent ATPase but totally lacks helicase activity.

DNA binding to RecD: role of the 1B domain in SF1B helicase activity.,Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley DB EMBO J. 2008 Aug 20;27(16):2222-9. Epub 2008 Jul 31. PMID:18668125^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley DB. DNA binding to RecD: role of the 1B domain in SF1B helicase activity. EMBO J. 2008 Aug 20;27(16):2222-9. Epub 2008 Jul 31. PMID:18668125 doi:10.1038/emboj.2008.144

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3k70"

@@ Line 2: / Line 2: @@
 <StructureSection load='3k70' size='340' side='right' caption='[[3k70]], [[Resolution|resolution]] 3.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3k70]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K70 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3k70]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K70 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w36|1w36]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2820, JW2788, recB, rorA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), b2822, JW2790, recC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), b2819, JW2787, recD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2820, JW2788, recB, rorA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b2822, JW2790, recC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b2819, JW2787, recD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_V Exodeoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.5 3.1.11.5] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3k70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k70 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k70 RCSB], [http://www.ebi.ac.uk/pdbsum/3k70 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3k70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k70 OCA], [http://pdbe.org/3k70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k70 RCSB], [http://www.ebi.ac.uk/pdbsum/3k70 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 20: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3k70 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3k70" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 37: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Ecoli]]
 [[Category: Exodeoxyribonuclease V]]
 [[Category: Saikrishnan, K]]

3k70

From Proteopedia

Revision as of 05:44, 9 February 2016

Crystal structure of the complete initiation complex of RecBCD

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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