Proteopedia - User contributions [en]

Leucyl-tRNA Synthetase

2018-05-15T16:16:07Z

Christian Fjeld: New page: <StructureSection load='4aq7' frame='true' size='340' side='right' caption='LARS (E coli) ternary complex with tRNAleu and leucyl adenylate analogue' scene='78/786656/Lars/2'> == General D...

<StructureSection load='4aq7' frame='true' size='340' side='right' caption='LARS (E coli) ternary complex with tRNAleu and leucyl adenylate analogue' scene='78/786656/Lars/2'>
== General Description ==
<scene name='78/786656/Total/1'>Leucyl tRNA synthetase (LARS)</scene> is a 97 kDa, class IA aminoacyl-tRNA synthetase (ARS) that catalyzes the ligation of leucine with tRNAleu in an ATP dependent mechanism. ARS are essential to all life as they charge amino acids onto cognate tRNAs in preparation for protein translation. This is step is a potential source of error in interpreting the genetic code as mischarged tRNAs will not be recognized during protein synthesis and could lead to nonfunctional proteins. As such, ARS have a high specificity for both tRNA and amino acids and contain an editing domain capable of hydrolyzing mischarged tRNA.

LARS is a cytoplasmic enzyme that is found as part of the multisynthetase complex in eukaryotes<ref>doi: 10.1007/978-3-319-46503-6_18</ref>. The multi-synthetase complex contains glutamylprolyl-tRNA synthetase (EPRS), isoleucyl (IARS), leucyl (LARS), glutaminyl (GARS), methionyl (MARS), lysyl (KARS), arginyl (RARS), and aspartyl (DARS) tRNA synthetases as well as p18, p38 and p43<ref>doi: 10.1016/S0006-291X(03)00485-6</ref>.
Multisynthetase complexes have also been seen in some archaea such as ''Thermococcus kodakarensis'' although the composition of the complex is not the same as eukaryotes<ref>doi: 10.1016/j.febslet.2012.05.039</ref>.
LARS has been shown to be involved with the mTOR pathways as a sensor of leucine levels within the cell<ref>doi: 10.1016/j.cell.2012.02.044</ref>.

=== Disease ===

Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.jmb.2009.04.073</ref>

== Structure ==

LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains. Together, these five domains carry out the task of aminoacylating uncharged tRNA and hydrolysing mischarged tRNA with a high specificity for tRNAleu.

=== Catalytic Domain ===
[[Image:CatalyticSite.png | thumb | Active site with leucyl adenylate analog and A76]]
The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNAleu. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNAleu is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.

[[Image:Scheme2.JPG]]

LARS, like all class I synthetases, is characterized by a Rossmann-fold catalytic domain with a central parallel β-sheet with α-helices on both faces. The active site catalyzes both the formation of the leucyl adenylate intermediate and the subsequent charging of leucine onto the terminal acceptor arm of the tRNA<ref>doi: 10.1093/emboj/19.10.2351</ref>. The binding pocket accommodates leucine as well as smaller amino acids such as isoleucine and valine. This allows tRNAleu to be mischarged with noncognate amino acids and must be corrected to ensure translational fidelity<ref>doi: 10.1016/S1097-2765(03)00098-4</ref>.

=== Editing Domain ===

The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNAleu, and releasing it for a subsequent round of aminoacylation. This <scene name='78/786656/Editing_conformation/1'>editing function</scene> allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows binding of aminoacylated tRNAs for error checking.

[[Image:Editing2.JPG]]

The binding pocket of the editing domain acts as a reciprocal sieve to the catalytic domain. The catalytic domain cannot distinguish between amino acids that are similar to, or smaller than leucine. The binding pocket of the editing site can accommodate these similar or smaller amino acids but excludes leucine due to a steric clash with a highly conserved theronine<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. Together, the catalytic site discriminates against larger or hydrophobically different amino acids and the editing site hydrolyzes smaller, structurally similar amino acids producing a very low error rate<ref>DOI: 10.1042/BJ20051249</ref>.

=== Anticodon Binding Domain ===

The <scene name='78/786656/Anticodon/1'>anticodon binding domain</scene> is essential for the fidelity of ARSs. However, there are 6 anticodons in ''E. coli'' that correspond to leucine including AAU, CUG, and GUG, so how does the enzyme recognize so many different tRNAs? This is accomplished by recognition of the D-loop by the enzyme rather than the actual anticodon. The anticodon binding domain interacts with <scene name='78/786656/Anticodon_binding_nucleotides/2'>10 nucleotides of the D-loop</scene>, 12-16 and 22-26, with U16 being essential for recognition. U16 specifically interacts with Arg718 and Lys711 within helix 4 forming hydrogen bonds.

The anticodon bindind domain is an all α helical domain made up of 5 helices in a bundle. Helices 3-5 form the tRNA recognition surface and are responsible for interaction with the D-loop of the incoming tRNA.

=== Leucine Specificity Domain ===

The <scene name='78/786656/Ls/1'>leucine-specific domain</scene>, specifically the KMSKS loop, plays a major role in catalysis in many species. The domain is highly variable between species but the KMSKS loop is highly conserved<ref>doi: 10.1038/nsmb.2317</ref>. In catalysis the domain functions by closing over the 3' terminal adenine of the tRNA, closing the catalytic site and allowing catalysis to take place.

In ''E.coli'' the leucine-specific domain is composed of 2 3-strand antiparallel β-sheets and pivots on a flexible loop. The KMSKS loop spans residues 619-623 and can contact A76 of the tRNA within the catalytic site<ref>doi: 10.1038/nsmb.2317</ref>. There is also a β-hairpin in ''E. coli'' that contacts bases 10 and 27 of the tRNA for stabilization<ref>doi: 10.1038/nsmb.2317</ref>.

=== Zinc Binding Domain ===

The <scene name='78/786656/Zn1/1'>zinc binding domain</scene> is a highly variable domain and different species have have 0-2 zinc binding motifs within the domain<ref>doi: 10.1093/emboj/19.10.2351</ref>. It is highly disordered in the apo state and, similar to the leucine-specific domain, closes and interacts with the tRNA in the aminoacylation state. It is unclear if the zinc ligand actively participates in catalysis or is required for the correct folding of the domain. Mutation of the zinc binding motif in some species, ''E. coli'', produces an inactive enzyme<ref>doi: 10.1093/emboj/19.10.2351</ref>.

== Evolutionary Conservation ==
LARS is essential for protein synthesis and as such is necessary for all cellular life and present in all three kingdoms of life. Eukaryal and archaeal LARS are similar and both are structurally different from bacterial LARS. Most of the differences occur in tRNA recognition sites while the core of the catalytic and editing domains are highly conserved. The differences between bacterial and archaeal tRNA, most notably the truncated variable arm in archaea, begin to explain the structural changes that are seen in the evolution of the enzyme<ref>doi: 10.1038/nsmb.2317</ref>.

A <scene name='78/786656/Conservation/2'>map of the conserved residues</scene> shows that there is a high degree of conservation in LARS, especially within the catalytic domain. The anticodon binding domain shows a higher variation. This is to be expected as there is a larger amount of variation in codon usage, most notable between bacteria and archaea/eukarya.

{{Template:ColorKey_ConSurf}}

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>

== 3D Structure of LARS ==

{{#tree:id=OrganizedByTopic|openlevels=0|

*LARS

**[[1wkb]] 
**[[2ajg]] 
**[[2ajh]] 
**[[2aji]] 
**[[2wfd]] Human editing domain 
**[[2wfe]] 
**[[2wfg]] 
**[[3o0a]] 
**[[4k47]] 
**[[4k48]] 
}}

== References ==
<references/>

Proteopedia:Structure Index/L-Q

2018-05-15T16:15:24Z

Christian Fjeld:

Updated: {{REVISIONDAY2}}-{{REVISIONMONTH}}-{{REVISIONYEAR}} (DD-MM-YYYY)
*[[Proteopedia:Structure_Index/num-A-C|Structure Index num-A-C]]
*[[Proteopedia:Structure_Index/D-K|Structure Index D-K]]
*[[Proteopedia:Structure_Index/L-Q|Structure Index L-Q]]
*[[Proteopedia:Structure_Index/R-Z|Structure Index R-Z]]

{{#tree:id=PDBTree| openlevels=0|
** L
*** [[L-rhamnose isomerase]]
*** [[Lac repressor]]
*** [[Lactate Dehydrogenase]]
*** [[Lactoferrin]]
*** [[Lactoperoxidase]]
*** [[Lactose Permease]]
*** [[Large T Antigen]]
*** [[Latrophilin]]
*** [[LDL receptor]]
*** [[LepA]]
*** [[Leptin]]
*** [[Leucine transporter]]
*** [[Leucyl-tRNA Synthetase]]
*** [[Leukocyte immunoglobulin-like receptor]] (LIR-1)
*** [[Leukocyte-associated immunoglobulin-like receptor]] (LAIR-1)
*** [[Leukotriene A4 Hydrolase]]
*** [[Leukotriene B4 hydroxydehydrogenase]]
*** [[Leukotriene C4 synthase]]
*** [[Lignin peroxidase]]
*** [[Lipase]]
*** [[Liver receptor homolog-1]] (LXR)
*** [[Liver X receptor]] (LRH-1)
*** [[Luciferase]]
*** [[Lysin]]
*** [[Lysine-specific histone demethylase]] (LSD)
*** [[Lysophosphatidic acid receptor]]
*** [[Lysozyme]]
*** [[Lysozyme 3D structures]]
** M
*** [[M2 protein]]
*** [[Macrophage inhibitory factor]] (MIF)
*** [[Magainin 2]]
*** [[Major histocompatibility complex]] (MHC)
*** [[Malate dehydrogenase]] (MDH)
*** [[Malate synthase]]
*** [[Maltose-binding protein]] (MBP)
*** [[Mandelate dehydrogenase]]
*** [[Mandelate racemase]]
*** [[Mandelate racemase/muconate lactonizing enzyme]]
*** [[Manganese peroxidase]]
*** [[Mannan-binding lectin serine protease]] (MASP)
*** [[Mannose-binding protein]]
*** [[Mannosidase]]
*** [[MAP kinase phosphatase]]
*** [[Matriptase]]
*** [[Matrix metalloproteinase]]
*** [[MDM2]]
*** [[MDM4]]
*** [[MECDP synthase]]
*** [[Mediator]]
*** [[Menin]]
*** [[MEP cytidylyltransferase]] (IspD)
*** [[Merlin]]
*** [[Met repressor]]
*** [[Metabotropic glutamate receptor]]
*** [[Metallothiol transferase FosB]]
*** [[Methane monooxygenase]]
*** [[Methanol dehydrogenase]]
*** [[Methionine gamma-lyase]] (MGL)
*** [[Methyl CpG binding protein]]
*** [[Methylamine dehydrogenase]]
*** [[Methylation utilization protein MauG]]
*** [[Methylcitrate synthase]]
*** [[Methylesterase]]
*** [[Microtubule-associated protein]]
*** [[Microtubule-associated serine/threonine kinase]] (MAST)
*** [[Mineralocorticoid receptor]]
*** [[Mitogen-activated protein kinase|Mitogen-activated protein kinase (MAPK)]]
*** [[Mitogen-activated protein kinase kinase|Mitogen-activated protein kinase kinase (MAP2K)]]
*** [[Mitogen-activated protein kinase kinase kinase|Mitogen-activated protein kinase kinase kinase (MAP3K)]]
*** [[ModG]]
*** [[Monoamine oxidase]]
*** [[Monoclonal Antibody]]
*** [[Monocyte chemoattractant protein]]
*** [[Monooxygenase]]
*** [[Muconate cycloisomerase]]
*** [[Mur ligase]]
*** [[Muscle LIM protein]]
*** [[Myeloperoxidase]]
*** [[Myocyte enhancer factor 2]] (MEF2)
*** [[Myoglobin]]
*** [[Myosin]]
*** [[Myosin light chain kinase]]
*** [[Myotilin]]
** N
*** [[NAC transcription factor]]
*** [[N-acetylornithine carbamoyltransferase]]
*** [[NAD kinase]]
*** [[NAD synthase]]
*** [[NAD(P) transhydrogenase]]
*** [[NADH peroxidase]]
*** [[NADH-quinone oxidoreductase]] (Complex I)
*** [[NADP-dependent malic enzyme]]
*** [[NADPH-Cytochrome P450 Reductase]]
*** [[NADPH dehydrogenase]] (OYE)
*** [[NalP]]
*** [[Nawaprin]]
*** [[Nebulin]]
*** [[NEDD8]]
*** [[Neprilysin]]
*** [[Netrin]]
*** [[Netrin receptor]]
*** [[Neuraminidase]]
*** [[Neurexin]]
*** [[Neuroglobin]]
*** [[Neuroligin]]
*** [[Neurophysin]]
*** [[Neuropilin]]
*** [[Neurotensin receptor]]
*** [[Neutrophil gelatinase-associated lipocalin]]
*** [[NF-kB]]
*** [[Nicotinic Acetylcholine Receptor]] (AChR)
*** [[Nisin]]
*** [[Nitrate reductase]]
*** [[Nitric Oxide Synthase]]
*** [[Nitrite reductase]]
*** [[Nitrile hydratase]]
*** [[Nitrogenase]]
*** [[Nitrophorin]]
*** [[Nitroreductase]]
*** [[NK cell receptor]]
*** [[NodS]]
*** [[Nonstructural protein]]
*** [[Nuclear receptor coactivator]]
*** [[Nuclear receptor corepressor]] (N-CoR)
*** [[Nuclear transcription factor Y]] (NF-Y)
*** [[Nucleolin]]
*** [[Nucleoplasmin]]
*** [[Nucleoporin]]
*** [[Nucleoprotein]]
*** [[Nucleoside diphosphate kinase]]
** O
*** [[Obscurin]]
*** [[O-GlcNAc transferase]]
*** [[Odorant binding protein]]
*** [[Oligopeptide-binding protein]]
*** [[Opioid receptor]]
*** [[Orexin and Orexin receptor]]
*** [[Organic hydroperoxide resistance protein]]
*** [[Ornithine carbamoyltransferase]]
*** [[Ornithine decarboxylase]]
*** [[Outer surface protein]] (Osp)
*** [[Ovalbumin]]
** P
*** [[P19]]
*** [[P53]]
*** [[P63]]
*** [[P73]]
*** [[Paired box protein]] (PAX)
*** [[Pal]]
*** [[Pantothenate kinase]]
*** [[Pantothenate synthetase]]
*** [[Papain]]
*** [[Parvalbumin]]
*** [[Paxillin]]
*** [[PcrH]]
*** [[PCSK9]]
*** [[PDZ and LIM domain protein]]
*** [[Penicillin acylase]]
*** [[Penicillin-binding protein]]
*** [[Penicillopepsin]]
*** [[Pentaerythritol tetranitrate reductase]]
*** [[Pepsin]]
*** [[Peptidase T]]
*** [[Peptide N-glycanase]] (PNGase)
*** [[Peptidyl-prolyl cis-trans isomerase]] (PPIase)
*** [[Peptidyl-tRNA hydrolase]] (PTH)
*** [[Peregrin]] (BRPF1)
*** [[Period circadian protein]] (PER)
*** [[Peroxiredoxin]]
*** [[Pertussis toxin]]
*** [[Pesticidal crystal protein]]
*** [[PPAR#Additional_3D_Structures_of_PPAR|Peroxisome Proliferator-Activated Receptors (PPAR)]]
*** [[Phage integrase]]
*** [[Phenylethanolamine N-methyltransferase]] (PNMT)
*** [[Phenylpyruvate decarboxylase]]
*** [[Pheromone binding protein]]
*** [[Pho4]]
*** [[PhoP-PhoQ]]
*** [[Phosphate-binding protein]]
*** [[Phosphocarrier protein]]
*** [[Phosphodiesterase]]
*** [[Phosphoenolpyruvate carboxykinase]] (PEPCK)
*** [[Phosphoenolpyruvate carboxylase]] (PEPC)
*** [[Phosphofructokinase (PFK)]]
*** [[Phosphoglucose isomerase]] (PGI)
*** [[Phosphoglycerate dehydrogenase]]
*** [[Phosphoglycerate Kinase]]
*** [[Phosphoglycerate Mutase]]
*** [[Phosphoinositide_3-Kinase#Additional_3D_Structures|Phosphoinositide 3-Kinase]] (PI3K)
*** [[Phosphoinositide phosphatase]]
*** [[Phospholamban]]
*** [[Phospholipase A1]] (PLA1)
*** [[Phospholipase A2|Phospholipase A2 (PLA2)]]
*** [[Phospholipase C]]
*** [[Phospholipase D]]
*** [[Phosphomannomutase]]
*** [[Phosphoribosylaminoimidazole carboxylase]] (PurE, PurK)
*** [[Phosphoribosyltransferase]]
*** [[Phosphoserine aminotransferase]]
*** [[Phosphoserine phosphatase]]
*** [[Phosphotransferase]]
*** [[Phosphotriesterase]]
*** [[Photosystem I]]
*** [[Photosystem II]]
*** [[Phycocyanin]]
*** [[Phycocyanobilin:ferredoxin oxidoreductase]]
*** [[Pilin]]
*** [[Plasmepsin]]
*** [[Plasmid segregation protein ParM]]
*** [[Plasminogen]]
*** [[Plasminogen activator]]
*** [[Plasminogen activator inhibitor]]
*** [[Platelet glycoprotein]] (CD42)
*** [[Plectin]]
*** [[Pleurotolysin]]
*** [[Plexin]]
*** [[Poliovirus receptor-related protein]] (Nectin)
*** [[Poly(A) Polymerase]]
*** [[Poly(A) RNA polymerase protein Cid1]]
*** [[Poly (ADP-ribose) glycohydrolase]] (PARG)
*** [[Poly (ADP-ribose) polymerase|Poly (ADP-ribose) polymerase (PARP)]]
*** [[Polyamine oxidase]]
*** [[Polygalacturonase]]
*** [[Polyhydroxybutyrate synthase]]
*** [[Polyneuridine Aldehyde Esterase]]
*** [[Porin]] (Omp)
*** [[Porphobilinogen Deaminase]]
*** [[Porphobilinogen synthase]]
*** [[Portal protein]]
*** [[Potassium_Channel#Additional_Structures_of_Potassium_Channels|Potassium Channel]]
*** [[Potassium channel toxin]]
*** [[Pre-mRNA-splicing factor]] (Prp)
*** [[Pregnane X receptor]] (PXR)
*** [[Preprotein translocase]]
*** [[Prestin]]
*** [[Prion]]
*** [[Profilin]]
*** [[Progesterone receptor]]
*** [[Prolactin]]
*** [[Prolactin receptor]]
*** [[Proliferating Cell Nuclear Antigen|Proliferating Cell Nuclear Antigen (PCNA)]]
*** [[Proline utilization A]] (PutA)
*** [[Prolyl Endopeptidase]]
*** [[Prolyl hydroxylase domain]]
*** [[Prostaglandin D synthase]] (PGDS)
*** [[Prostaglandin E synthase]] (PGES)
*** [[Prostaglandin F synthase]] (AKR1C3)
*** [[Proteasome]]
*** [[Protegrin]]
*** [[Protein disulfide oxidoreductase]]
*** [[Protein G]]
*** [[Protein kinase C]]
*** [[Protein kinase Spk1]] (Rad53)
*** [[Protein Nef]]
*** [[Protein phosphatase]]
*** [[Protein Rev]]
*** [[Proteinase]]
*** [[Proto-oncogene serine/threonine-protein kinase]] (Pim-1)
*** [[Proto-oncogene tyrosine-protein kinase]]
*** [[Pseudechetoxin]]
*** [[Pseudoazurin]]
*** [[Pseudopilin]]
*** [[Pteridine reductase]]
*** [[Purine nucleoside phosphorylase]] (PNP)
*** [[Purine repressor]] (PurR)
*** [[Pyranose oxidase]]
*** [[Pyridoxal kinase]]
*** [[Pyridoxine 5'-phosphate oxidase]]
*** [[Pyrin domain]]
*** [[Pyrroline-5-carboxylate dehydrogenase]]
*** [[Pyrroline-5-carboxylate reductase]]
*** [[Pyrrolysyl-tRNA synthetase]]
*** [[Pyruvate-ferredoxin oxidoreductase]]
*** [[Pyruvate decarboxylase]]
*** [[Pyruvate dehydrogenase]]
*** [[Pyruvate dehydrogenase kinase]]
*** [[Pyruvate Kinase]]
*** [[Pyruvate phosphate dikinase]]
** Q
*** [[Quinone reductase]]
}}

2018-05-03T13:47:27Z

Christian Fjeld:

2018-04-30T21:50:07Z

Christian Fjeld:

== General Description ==
<StructureSection load='4aq7' frame='true' size='340' side='right' caption='LARS (E coli) ternary complex with tRNAleu and leucyl adenylate analogue' scene='78/786656/Lars/1'>
Leucyl tRNA synthetase (LARS) is a 97 kDa, class IA aminoacyl-tRNA synthetase (ARS) that catalyzes the ligation of leucine with tRNAleu in an ATP dependent mechanism. LARS is a cytoplasmic enzyme that is found as part of the multisynthetase complex in mammals<ref>doi: 10.1007/978-3-319-46503-6_18</ref>. LARS has been shown to be involved with the mTOR pathways as a sensor of leucine levels within the cell<ref>doi: 10.1016/j.cell.2012.02.044</ref>.

Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.ajhg.2013.03.007</ref>

== Structure ==

=== Catalytic Domain ===

=== Editing Domain ===

=== Anticodon Binding Domain ===

== Disease ==

</StructureSection>
== 3D Structure of LARS ==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*LARS

**[[1wkb]] 
**[[2ajg]] 
**[[2ajh]] 
**[[2aji]] 
**[[2wfd]] 
**[[2wfe]] 
**[[2wfg]] 
**[[3o0a]] 
**[[4k47]] 
**[[4k48]] 
}}
== References ==
<references/>