Protein Hfq: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky

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-<StructureSection load='4ht9' size='340' side='right' caption='Structure of human pentameric SAP  (green, grey, pink, yellow, magenta) complex with AMP and Ca+2 ions (green) (PDB code [[4ht9]])' scene=''>
+<StructureSection load='4ht9' size='340' side='right' caption='Structure of E. coli hexameric Hfq  complex with poly(A) RNA and poly(U) RNA (PDB code [[4ht9]])' scene='87/875687/Cv/1'>
 == Function ==
-'''Protein Hfq''' (Hfq) ('''H'''ost '''F'''actor for '''Q'''β) or '''RNA-binding protein Hfq''' is stimulating base-pairing between sRNA and target mRNA by binding both RNAs via three RNA-binding surfaces.  Hfq is found in enteric bacteria<ref>PMID:30487269</ref>.  SAP binds in a calcium-dependent fashion to a variety of ligands.
+'''Protein Hfq''' (Hfq) ('''H'''ost '''F'''actor for '''Q'''β) or '''RNA-binding protein Hfq''' is stimulating base-pairing between sRNA and target mRNA by binding both RNAs via three RNA-binding surfaces.  Hfq is found in enteric bacteria<ref>PMID:30487269</ref>.  Hfq binds RNA via poly(A-R-N) triplets where A is adenosine, R is purine nucleotide and N is any nucleotide<ref>PMID:19889981</ref>.
 == Relevance ==
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 == Structural highlights ==
-<scene name='87/875651/Cv/5'>The 3D structure of a complex of SAP with the small molecule ligand AMP</scene> shows the nucleotide phosphate group bridging two Ca+2 ions and forming hydrogen bonds to Asn, Gln and Try residues of SAP  <ref>PMID:9217261</ref>.
+The biological assembly of Protein Hfq from ''E. coli'' is <scene name='87/875687/Cv/2'>homohexamer</scene> (PDB code [[4ht9]]). The 3D structure of the complex between Hfq and <scene name='87/875687/Cv/5'>poly(A) RNA and poly(U) RNA</scene> shows the poly(A) binding at the distal face of Hfq and poly(U) binding at its proximal face. For the poly(A) A-R-N binding site the A site shows <scene name='87/875687/Cv/4'>hydrogen bonding to Gln and Lys</scene>.  The <scene name='87/875687/Cv/6'>R site shows stacking interactions as well as hydrogen bonding</scene>. The N site does not show any interaction. <scene name='87/875687/Cv/7'>The poly(U) binding site of Hfq is a classical uridine binding pocket with both stacking and hydrogen bonding interactions</scene><ref>PMID:23605038</ref>.
-</StructureSection>
 == 3D Structures of protein Hfq ==
-Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+[[Protein Hfq 3D structures]]
-{{#tree:id=OrganizedByTopic|openlevels=0|
-*Protein Hfq
-**[[1hk9]], [[2y90]], [[2yht]], [[3qhs]], [[4rcb]], [[4rcc]], [[6bdg]] – EcHfq  –  ''Escherichia coli'' <br />
-**[[4jli]], [[4jri]], [[4jrk]], [[4juv]] – EcHfq  (mutant)<br />
-**[[1u1s]], [[1u1t]], [[4j6y]], [[6xyj]] – PaHfq  –  ''Pseudomonas aeruginosa''<br />
-**[[3inz]], [[3m4g]], [[4mml]], [[4mmk]], [[5i21]] – PaHfq  (mutant)<br />
-**[[2ylb]] – StHfq  –  ''Salmonella typhimurium''<br />
-**[[6gwk]] – Hfq  –  ''Caulobacter crescentus''<br />
-**[[4nl2]] – LmHfq – ''Listeria monocytogenes''<br />
-**[[4noy]] – LmHfq  (mutant)<br />
-**[[5szd]] – AaHfq – ''Aquifex aeolicus''<br />
-**[[3sb2]] – Hfq  - ''Herbaspirillum seropedicae''<br />
-**[[1kq1]] – SaHfq – ''Staphylococcus aureus''<br />
-**[[2qtx]], [[4x9c]] – MjHfq – ''Methanococcus jannaschii''<br />
-**[[3hfn]] – Hfq  - ''Anabaena''<br />
-*Protein Hfq complex with nucleotide
-**[[3res]] – EcHfq  + ADP<br />
-**[[3qo3]] – EcHfq  + ATP<br />
-**[[4pno]] – EcHfq  + UMP<br />
-**[[4j6x]] – PaHfq  + UTP<br />
-**[[3qui]] – PaHfq  + ADPNP<br />
-**[[4j5y]] – PaHfq  + ATP<br />
-**[[4j6w]] – PaHfq  + CTP<br />
-**[[2ylc]] – StHfq  + UMP<br />
-**[[5dy9]] – MjHfq  (mutant) + AMP<br />
-**[[4x9d]] – MjHfq + UMP<br />
-*Protein Hfq other complexes
-**[[6qlb]] – EcHfq + calpain <br />
-**[[3vu3]] – EcHfq + catalase <br />
-**[[3gib]], [[4ht8]] – EcHfq + poly(A)<br />
-**[[4ht9]], [[5new]] – EcHfq + poly(A) + poly(U)<br />
-**[[3rer]] – EcHfq + poly(U) + ADP<br />
-**[[4qvc]], [[4qvd]] – EcHfq + RNA<br />
-**[[5uk7]] – EcHfq + DNA<br />
-**[[3ahu]], [[3hsb]] – Hfq + RNA  –  ''Bacillus subtilis''<br />
-**[[6o1k]], [[6o1l]], [[6o1m]] – PaHfq  + Crc + RNA – Cryo EM<br />
-**[[4v2s]] – StHfq + sRNA<br />
-**[[4y91]] – Hfq + poly(U) – ''Thermotoga maritima''<br />
-**[[4nl3]] – LmHfq + poly(U) <br />
-**[[5sze]] – AaHfq + poly(U) <br />
-**[[1kq2]] – SaHfq + RNA <br />
-}}
 == References ==
 <references/>
+</StructureSection>
 [[Category:Topic Page]]