1zl3
From Proteopedia
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|PDB= 1zl3 |SIZE=350|CAPTION= <scene name='initialview01'>1zl3</scene>, resolution 2.80Å | |PDB= 1zl3 |SIZE=350|CAPTION= <scene name='initialview01'>1zl3</scene>, resolution 2.80Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span> |
|GENE= truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB]</span> | ||
}} | }} | ||
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[[Category: Hoang, C.]] | [[Category: Hoang, C.]] | ||
[[Category: Mueller, E G.]] | [[Category: Mueller, E G.]] | ||
| - | [[Category: SO4]] | ||
[[Category: inter-domain coupling]] | [[Category: inter-domain coupling]] | ||
[[Category: product release]] | [[Category: product release]] | ||
[[Category: rna-modification]] | [[Category: rna-modification]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:38:08 2008'' |
Revision as of 22:38, 30 March 2008
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| , resolution 2.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | truB (Escherichia coli) | ||||||
| Activity: | Pseudouridylate synthase, with EC number 4.2.1.70 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Coupling of active site motions and RNA binding
Overview
The pseudouridine synthase TruB is responsible for the universally conserved post-transcriptional modification of residue 55 of elongator tRNAs. In addition to the active site, the "thumb", a peripheral domain unique to the TruB family of enzymes, makes extensive interactions with the substrate. To coordinate RNA binding and release with catalysis, the thumb may be able to sense progress of the reaction in the active site. To establish whether there is a structural correlate of communication between the active site and the RNA-sequestering thumb, we have solved the structure of a catalytically inactive point mutant of TruB in complex with a substrate RNA, and compared it to the previously determined structure of an active TruB bound to a reaction product. Superposition of the two structures shows that they are extremely similar, except in the active site and, intriguingly, in the relative position of the thumb. Because the two structures were solved using isomorphous crystals, and because the thumb is very well ordered in both structures, the displacement of the thumb we observe likely reflects preferential propagation of active site perturbations to this RNA-binding domain. One of the interactions between the active site and the thumb involves an active site residue whose hydrogen-bonding status changes during the reaction. This may allow the peripheral RNA-binding domain to monitor progress of the pseudouridylation reaction.
About this Structure
1ZL3 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain., Hoang C, Hamilton CS, Mueller EG, Ferre-D'Amare AR, Protein Sci. 2005 Aug;14(8):2201-6. Epub 2005 Jun 29. PMID:15987897
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