2r1j

From Proteopedia

(Difference between revisions)

Revision as of 04:11, 2 July 2021

Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T

Structural highlights

2r1j is a 4 chain structure with sequence from Bpp22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	c2 (BPP22)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPC2_BPP22] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development.

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 P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps to direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. We describe the 1.6 A X-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2. This operator has an A-T base pair at position 9L and a T-A base pair at position 9R and is termed DNA9T. Direct readout: nondirectional van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD-DNA9T complex suggests that sequence-specificity arises substantially from lock-and-key interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5'-TTAA-3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational changes. Protein-DNA hydrogen bonding plays a secondary role in specificity. Indirect readout: it is known that the noncontacted bases in the center of the complex are important determinants of affinity. The protein induces a transition of the noncontacted region from B-DNA to B'-DNA. The B' state is characterized by a narrow minor groove and a zigzag spine of hydration. The free energy of the transition from B- to B'-DNA is known to depend on the sequence. Thus, the observed DNA conformation and hydration allows for the formulation of a predictive model of the indirect readout phenomenon.

P22 c2 repressor-operator complex: mechanisms of direct and indirect readout.,Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD Biochemistry. 2008 Feb 26;47(8):2325-38. Epub 2008 Feb 1. PMID:18237194^[1]

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

References

↑ Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD. P22 c2 repressor-operator complex: mechanisms of direct and indirect readout. Biochemistry. 2008 Feb 26;47(8):2325-38. Epub 2008 Feb 1. PMID:18237194 doi:10.1021/bi701826f

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2r1j"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T==
-<StructureSection load='2r1j' size='340' side='right' caption='[[2r1j]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
+<StructureSection load='2r1j' size='340' side='right'caption='[[2r1j]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r1j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r1j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1J FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10754 BPP22])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10754 BPP22])</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=2r1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1j OCA], [http://pdbe.org/2r1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r1j RCSB], [http://www.ebi.ac.uk/pdbsum/2r1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1j ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1j OCA], [https://pdbe.org/2r1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1j RCSB], [https://www.ebi.ac.uk/pdbsum/2r1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPC2_BPP22 RPC2_BPP22]] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development.
+[[https://www.uniprot.org/uniprot/RPC2_BPP22 RPC2_BPP22]] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 </StructureSection>
 [[Category: Bpp22]]
+[[Category: Large Structures]]
 [[Category: Hsiao, C]]
 [[Category: Koudelka, G B]]

2r1j

From Proteopedia

Revision as of 04:11, 2 July 2021

Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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