1u3d: Difference between revisions

Latest revision as of 06:37, 23 August 2023

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound

Structural highlights

1u3d is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.45Å
Ligands:	ANP, CL, FAD, MG, NDS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CRY1_ARATH Mediates blue light-induced gene expression through the inhibition of COP1-mediated degradation of the transcription factor BIT1. Involved in blue light-dependent stomatal opening, CHS gene expression, inhibition of stem growth and increase of root growth.^[1] ^[2] ^[3] ^[4] ^[5]

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

Signals generated by cryptochrome (CRY) blue-light photoreceptors are responsible for a variety of developmental and circadian responses in plants. The CRYs are also identified as circadian blue-light photoreceptors in Drosophila and components of the mammalian circadian clock. These flavoproteins all have an N-terminal domain that is similar to photolyase, and most have an additional C-terminal domain of variable length. We present here the crystal structure of the photolyase-like domain of CRY-1 from Arabidopsis thaliana. The structure reveals a fold that is very similar to photolyase, with a single molecule of FAD noncovalently bound to the protein. The surface features of the protein and the dissimilarity of a surface cavity to that of photolyase account for its lack of DNA-repair activity. Previous in vitro experiments established that the photolyase-like domain of CRY-1 can bind Mg.ATP, and we observe a single molecule of an ATP analog bound in the aforementioned surface cavity, near the bound FAD cofactor. The structure has implications for the signaling mechanism of CRY blue-light photoreceptors.

Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.,Brautigam CA, Smith BS, Ma Z, Palnitkar M, Tomchick DR, Machius M, Deisenhofer J Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12142-7. Epub 2004 Aug 6. PMID:15299148^[6]

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

References

↑ Malhotra K, Kim ST, Batschauer A, Dawut L, Sancar A. Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity. Biochemistry. 1995 May 23;34(20):6892-9. PMID:7756321
↑ Ahmad M, Jarillo JA, Smirnova O, Cashmore AR. Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism. Nature. 1998 Apr 16;392(6677):720-3. PMID:9565033 doi:https://dx.doi.org/10.1038/33701
↑ Mao J, Zhang YC, Sang Y, Li QH, Yang HQ. From The Cover: A role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening. Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12270-5. Epub 2005 Aug 10. PMID:16093319 doi:https://dx.doi.org/0501011102
↑ Canamero RC, Bakrim N, Bouly JP, Garay A, Dudkin EE, Habricot Y, Ahmad M. Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana. Planta. 2006 Oct;224(5):995-1003. Epub 2006 May 9. PMID:16703358 doi:https://dx.doi.org/10.1007/s00425-006-0280-6
↑ Hong SH, Kim HJ, Ryu JS, Choi H, Jeong S, Shin J, Choi G, Nam HG. CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis. Plant J. 2008 Aug;55(3):361-71. Epub 2008 Apr 4. PMID:18397371 doi:https://dx.doi.org/TPJ3508
↑ Brautigam CA, Smith BS, Ma Z, Palnitkar M, Tomchick DR, Machius M, Deisenhofer J. Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12142-7. Epub 2004 Aug 6. PMID:15299148 doi:10.1073/pnas.0404851101

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Malhotra K, Kim ST, Batschauer A, Dawut L, Sancar A. Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity. Biochemistry. 1995 May 23;34(20):6892-9. PMID:7756321

[2] Ahmad M, Jarillo JA, Smirnova O, Cashmore AR. Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism. Nature. 1998 Apr 16;392(6677):720-3. PMID:9565033 doi:https://dx.doi.org/10.1038/33701

[3] Mao J, Zhang YC, Sang Y, Li QH, Yang HQ. From The Cover: A role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening. Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12270-5. Epub 2005 Aug 10. PMID:16093319 doi:https://dx.doi.org/0501011102

[4] Canamero RC, Bakrim N, Bouly JP, Garay A, Dudkin EE, Habricot Y, Ahmad M. Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana. Planta. 2006 Oct;224(5):995-1003. Epub 2006 May 9. PMID:16703358 doi:https://dx.doi.org/10.1007/s00425-006-0280-6

[5] Hong SH, Kim HJ, Ryu JS, Choi H, Jeong S, Shin J, Choi G, Nam HG. CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis. Plant J. 2008 Aug;55(3):361-71. Epub 2008 Apr 4. PMID:18397371 doi:https://dx.doi.org/TPJ3508

[6] Brautigam CA, Smith BS, Ma Z, Palnitkar M, Tomchick DR, Machius M, Deisenhofer J. Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12142-7. Epub 2004 Aug 6. PMID:15299148 doi:10.1073/pnas.0404851101

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='1u3d' size='340' side='right'caption='[[1u3d]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1u3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U3D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1u3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U3D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDS:ETHYL+DIMETHYL+AMMONIO+PROPANE+SULFONATE'>NDS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u3c|1u3c]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDS:ETHYL+DIMETHYL+AMMONIO+PROPANE+SULFONATE'>NDS</scene></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=1u3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u3d OCA], [https://pdbe.org/1u3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u3d RCSB], [https://www.ebi.ac.uk/pdbsum/1u3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u3d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CRY1_ARATH CRY1_ARATH]] Mediates blue light-induced gene expression through the inhibition of COP1-mediated degradation of the transcription factor BIT1. Involved in blue light-dependent stomatal opening, CHS gene expression, inhibition of stem growth and increase of root growth.<ref>PMID:7756321</ref> <ref>PMID:9565033</ref> <ref>PMID:16093319</ref> <ref>PMID:16703358</ref> <ref>PMID:18397371</ref>
+[https://www.uniprot.org/uniprot/CRY1_ARATH CRY1_ARATH] Mediates blue light-induced gene expression through the inhibition of COP1-mediated degradation of the transcription factor BIT1. Involved in blue light-dependent stomatal opening, CHS gene expression, inhibition of stem growth and increase of root growth.<ref>PMID:7756321</ref> <ref>PMID:9565033</ref> <ref>PMID:16093319</ref> <ref>PMID:16703358</ref> <ref>PMID:18397371</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Brautigam, C A]]
+[[Category: Brautigam CA]]
-[[Category: Deisenhofer, J]]
+[[Category: Deisenhofer J]]
-[[Category: Ma, Z]]
+[[Category: Ma Z]]
-[[Category: Machius, M]]
+[[Category: Machius M]]
-[[Category: Palnitkar, M]]
+[[Category: Palnitkar M]]
-[[Category: Smith, B S]]
+[[Category: Smith BS]]
-[[Category: Tomchick, D R]]
+[[Category: Tomchick DR]]
-[[Category: Amppnp]]
-[[Category: Photolyase]]
-[[Category: Signaling protein]]

1u3d: Difference between revisions

Latest revision as of 06:37, 23 August 2023

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools