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==Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II==
==Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II==
<StructureSection load='5egb' size='340' side='right' caption='[[5egb]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
<StructureSection load='5egb' size='340' side='right'caption='[[5egb]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5egb]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EGB FirstGlance]. <br>
<table><tr><td colspan='2'>[[5egb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EGB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.977&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5eh2|5eh2]], [[5ei9|5ei9]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=5egb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egb OCA], [https://pdbe.org/5egb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5egb RCSB], [https://www.ebi.ac.uk/pdbsum/5egb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5egb ProSAT]</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=5egb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egb OCA], [http://pdbe.org/5egb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5egb RCSB], [http://www.ebi.ac.uk/pdbsum/5egb PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PRDM9_HUMAN PRDM9_HUMAN]] Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity).
[https://www.uniprot.org/uniprot/PRDM9_HUMAN PRDM9_HUMAN] Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The multidomain zinc finger (ZnF) protein PRDM9 (PRD1-BF1-RIZ1 homologous domain-containing 9) is thought to influence the locations of recombination hot spots during meiosis by sequence-specific DNA binding and trimethylation of histone H3 Lys4. The most common variant of human PRDM9, allele A (hPRDM9A), recognizes the consensus sequence 5'-NCCNCCNTNNCCNCN-3'. We cocrystallized ZnF8-12 of hPRDM9A with an oligonucleotide representing a known hot spot sequence and report the structure here. ZnF12 was not visible, but ZnF8-11, like other ZnF arrays, follows the right-handed twist of the DNA, with the alpha helices occupying the major groove. Each alpha helix makes hydrogen-bond (H-bond) contacts with up to four adjacent bases, most of which are purines of the complementary DNA strand. The consensus C:G base pairs H-bond with conserved His or Arg residues in ZnF8, ZnF9, and ZnF11, and the consensus T:A base pair H-bonds with an Asn that replaces His in ZnF10. Most of the variable base pairs (N) also engage in H bonds with the protein. These interactions appear to compensate to some extent for changes from the consensus sequence, implying an adaptability of PRDM9 to sequence variations. We investigated the binding of various alleles of hPRDM9 to different hot spot sequences. Allele C was found to bind a C-specific hot spot with higher affinity than allele A bound A-specific hot spots, perhaps explaining why the former is dominant in A/C heterozygotes. Allele L13 displayed higher affinity for several A-specific sequences, allele L9/L24 displayed lower affinity, and allele L20 displayed an altered sequence preference. These differences can be rationalized structurally and might contribute to the variation observed in the locations and activities of meiotic recombination hot spots.


Structural basis for human PRDM9 action at recombination hot spots.,Patel A, Horton JR, Wilson GG, Zhang X, Cheng X Genes Dev. 2016 Feb 1;30(3):257-65. doi: 10.1101/gad.274928.115. PMID:26833727<ref>PMID:26833727</ref>
==See Also==
 
*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5egb" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Histone-lysine N-methyltransferase]]
[[Category: Homo sapiens]]
[[Category: Cheng, X]]
[[Category: Large Structures]]
[[Category: Horton, J R]]
[[Category: Cheng X]]
[[Category: Patel, A]]
[[Category: Horton JR]]
[[Category: Wilson, G G]]
[[Category: Patel A]]
[[Category: Zhang, X]]
[[Category: Wilson GG]]
[[Category: Protein-dna complex]]
[[Category: Zhang X]]
[[Category: Transcription-dna complex]]
[[Category: Zinc finger protein]]

Latest revision as of 15:28, 6 March 2024

Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence IIHuman PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II

Structural highlights

5egb is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.977Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRDM9_HUMAN Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity).

See Also

5egb, resolution 1.98Å

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