This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2vuu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:33, 25 June 2020

Crystal structure of NADP-bound NmrA-AreA zinc finger complex

Structural highlights

2vuu is a 16 chain structure with sequence from A. nidulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2vus, 2vut
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NMRA_EMENI] May be a redox sensor protein. Has much higher affinity for NAD(P) than for NAD(P)H. Has similar affinity for NAD and NADP. Negative transcriptional regulator involved in the post-transcriptional modulation of the GATA-type transcription factor areA, forming part of a system controlling nitrogen metabolite repression (By similarity). Interferes with the interaction between areA and target DNA. Overexpression leads to areA inhibition.^[1] ^[2] ^[3] ^[4] [AREA_EMENI] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.^[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

Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.

Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.,Kotaka M, Johnson C, Lamb HK, Hawkins AR, Ren J, Stammers DK J Mol Biol. 2008 Aug 29;381(2):373-82. Epub 2008 Jun 5. PMID:18602114^[6]

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

References

↑ Wong KH, Hynes MJ, Todd RB, Davis MA. Transcriptional control of nmrA by the bZIP transcription factor MeaB reveals a new level of nitrogen regulation in Aspergillus nidulans. Mol Microbiol. 2007 Oct;66(2):534-51. Epub 2007 Sep 10. PMID:17854403 doi:http://dx.doi.org/10.1111/j.1365-2958.2007.05940.x
↑ Lamb HK, Leslie K, Dodds AL, Nutley M, Cooper A, Johnson C, Thompson P, Stammers DK, Hawkins AR. The negative transcriptional regulator NmrA discriminates between oxidized and reduced dinucleotides. J Biol Chem. 2003 Aug 22;278(34):32107-14. Epub 2003 May 22. PMID:12764138 doi:10.1074/jbc.M304104200
↑ Lamb HK, Ren J, Park A, Johnson C, Leslie K, Cocklin S, Thompson P, Mee C, Cooper A, Stammers DK, Hawkins AR. Modulation of the ligand binding properties of the transcription repressor NmrA by GATA-containing DNA and site-directed mutagenesis. Protein Sci. 2004 Dec;13(12):3127-38. Epub 2004 Nov 10. PMID:15537757 doi:10.1110/ps.04958904
↑ Kotaka M, Johnson C, Lamb HK, Hawkins AR, Ren J, Stammers DK. Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA. J Mol Biol. 2008 Aug 29;381(2):373-82. Epub 2008 Jun 5. PMID:18602114 doi:http://dx.doi.org/10.1016/j.jmb.2008.05.077
↑ Kudla B, Caddick MX, Langdon T, Martinez-Rossi NM, Bennett CF, Sibley S, Davies RW, Arst HN Jr. The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specificity of gene activation alter a loop residue of a putative zinc finger. EMBO J. 1990 May;9(5):1355-64. PMID:1970293
↑ Kotaka M, Johnson C, Lamb HK, Hawkins AR, Ren J, Stammers DK. Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA. J Mol Biol. 2008 Aug 29;381(2):373-82. Epub 2008 Jun 5. PMID:18602114 doi:http://dx.doi.org/10.1016/j.jmb.2008.05.077

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/2vuu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of NADP-bound NmrA-AreA zinc finger complex==
-<StructureSection load='2vuu' size='340' side='right' caption='[[2vuu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='2vuu' size='340' side='right'caption='[[2vuu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vuu]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VUU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vuu]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VUU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vus|2vus]], [[2vut|2vut]]</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=2vuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vuu OCA], [http://pdbe.org/2vuu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vuu RCSB], [http://www.ebi.ac.uk/pdbsum/2vuu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vuu ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vuu OCA], [http://pdbe.org/2vuu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vuu RCSB], [http://www.ebi.ac.uk/pdbsum/2vuu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vuu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: A. nidulans]]
+[[Category: Large Structures]]
 [[Category: Hawkins, A R]]
 [[Category: Johnson, C]]

2vuu

From Proteopedia

Revision as of 08:33, 25 June 2020

Crystal structure of NADP-bound NmrA-AreA zinc finger complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox