Editing Pyrrolysine

{{redirect|Pyl}}
{{distinguish|Pyrolysis}}
{{chembox
| Verifiedfields = changed
| Watchedfields  = changed
| verifiedrevid  = 464378022
| ImageFile1     = Pyrrolysine.svg
| ImageSize1     = 240px
| ImageFile2     = Pyrrolysine-from-PDB-3D-bs-17.png
| ImageSize2     = 240px
| IUPACName      = Pyrrolysine<ref>{{cite book |author=[[International Union of Pure and Applied Chemistry]] |date=2014 |title=Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 |publisher=[[Royal Society of Chemistry|The Royal Society of Chemistry]] |pages=1392 |doi=10.1039/9781849733069 |isbn=978-0-85404-182-4}}</ref>
|SystematicName=''N''<sup>6</sup>-{[(2''R'',3''R'')-3-methyl-3,4-dihydro-2''H''-pyrrol-2-yl]carbonyl}-<small>L</small>-lysine
| OtherNames     = (2''S'')-2-amino-6-{[(2''R'',3''R'')-3-methyl-3,4-dihydro-2''H''-pyrrole-2-carbonyl]-amino}-hexanoic acid<br>''N''<sup>6</sup>-(4-methyl-1,2-didehydropyrrolidine-5-carboxyl)-<small>L</small>-lysine<br>monomethylamine methyltransferase cofactor lysine adduct
| Section1       = {{Chembox Identifiers
|   ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}}
| ChemSpiderID = 4574156
| KEGG_Ref = {{keggcite|correct|kegg}}
| KEGG = C16138
| InChI = 1/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9+,10-/m1/s1
| InChIKey = ZFOMKMMPBOQKMC-KXUCPTDWBO
| StdInChI_Ref = {{stdinchicite|correct|chemspider}}
| StdInChI = 1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9+,10-/m1/s1
| StdInChIKey_Ref = {{stdinchicite|correct|chemspider}}
| StdInChIKey = ZFOMKMMPBOQKMC-KXUCPTDWSA-N
| CASNo_Ref = {{cascite|correct|CAS}}
| CASNo = 448235-52-7
| UNII_Ref = {{fdacite|correct|FDA}}
| UNII = H3214Y96LP
|   PubChem = 5460671
|   ChEBI_Ref = {{ebicite|changed|EBI}}
| ChEBI = 21860
| SMILES = C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@@H](C(=O)O)N
| SMILES1 = O=C(NCCCC[C@@H](C(=O)[O-])[NH3+])[C@@H]1/N=C\C[C@H]1C
| SMILES1_Comment = [[Zwitterion]]
}}
| Section2       = {{Chembox Properties
|  C=12|H=21|N=3|O=3
|   MolarMass = 255.313 g/mol
|   Appearance =
|   Density =
|   MeltingPt =
|   BoilingPt =
|   Solubility =
  }}
}}
[[File:Pyrrolysine-spin.gif|thumb|Pyrrolysine ball and stick model spinning]]
'''Pyrrolysine''' (symbol '''Pyl''' or '''O'''<ref>{{cite web | url = http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html | title = Nomenclature and Symbolism for Amino Acids and Peptides | publisher = IUPAC-IUB Joint Commission on Biochemical Nomenclature | year = 1983 | access-date = 5 March 2018 | archive-url = https://web.archive.org/web/20081009023202/http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html | archive-date = 9 October 2008 | url-status = dead }}</ref>), encoded by the 'amber' [[stop codon]] '''UAG''', is a [[proteinogenic amino acid]] that is used in some [[methanogen]]ic [[archaea]] and in [[bacteria]].<ref>{{Cite web|url=http://www.chem.qmul.ac.uk/iubmb/newsletter/2009.html#item35|publisher=Biochemical Nomenclature Committee of IUPAC and NC-IUBMB|title=Newsletter 2009|editor=Richard Cammack|year=2009|at=Pyrrolysine|access-date=2012-04-16|archive-url=https://web.archive.org/web/20170912194130/http://www.chem.qmul.ac.uk/iubmb/newsletter/2009.html#item35|archive-date=2017-09-12|url-status=dead}}</ref><ref name="pmid20847933">{{Cite journal|title = Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea|journal = Archaea|date = 2010-01-01|issn = 1472-3646|pmc = 2933860|pmid = 20847933|volume = 2010|doi = 10.1155/2010/453642|first1 = Michael|last1 = Rother|first2 = Joseph A.|last2 = Krzycki|pages=1–14|doi-access = free}}</ref> It consists of [[lysine]] with a 4-methylpyrroline-5-carboxylate in amide linkage with the <sup>ε</sup>N of the lysine. Its [[pyrroline]] side-chain is similar to that of lysine in being basic and positively charged at neutral pH.<ref name=Hao>{{cite journal|title=A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase|journal=Science|date=2002-05-24|volume=296|issue=5572|pages=1462–1466|doi=10.1126/science.1069556|pmid=12029132|bibcode = 2002Sci...296.1462H |last2=Gong|last3=Ferguson|last4=James|last5=Krzycki|last6=Chan|last1=Hao|first1=Bing|s2cid=35519996}}</ref><ref name=Soares>{{cite journal|title=The residue mass of <small>L</small>-pyrrolysine in three distinct methylamine methyltransferases|date=2005-11-04|doi=10.1074/jbc.M506402200|volume=280|pages=36962–36969|pmid=16096277|issue=44|journal=The Journal of Biological Chemistry|last1=Soares|first1=J. A.|last2=Zhang|first2=L|last3=Pitsch|first3=R. L.|last4=Kleinholz|first4=N. M.|last5=Jones|first5=R. B.|last6=Wolff|first6=J. J.|last7=Amster|first7=J|last8=Green-Church|first8=K. B.|last9=Krzycki|first9=J. A.|doi-access=free}}</ref>

==Genetics==
Nearly all genes are translated using only 20 standard [[amino acid]] building blocks. Two unusual genetically-encoded amino acids are [[selenocysteine]] and pyrrolysine. Pyrrolysine was discovered in 2002 at the active site of [[methyltransferase]] enzyme from a methane-producing archeon, ''[[Methanosarcina barkeri]]''.<ref>{{cite journal|title=Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA |journal=Science |date=2002-05-24|volume=296|issue=5572|pages=1459–1462|doi=10.1126/science.1069588 |pmid=12029131 |bibcode = 2002Sci...296.1459S |last1=Srinivasan |first1=G |last2=James |first2=C. M. |last3=Krzycki |first3=J. A. |s2cid=28593085 }}</ref><ref name=Hao /> This amino acid is encoded by UAG (normally a stop codon), and its synthesis and incorporation into protein is mediated via the biological machinery encoded by the ''pylTSBCD'' [[Metabolic gene cluster|cluster of genes]].<ref name="pmid20847933" />

==Synthesis==
Pyrrolysine is synthesized ''in vivo'' by joining two molecules of <small>L</small>-lysine. One molecule of lysine is first converted to [[3-Methylornithine|(3''R'')-3-methyl-<small>D</small>-ornithine]], which is then ligated to a second lysine. An NH<sub>2</sub> group is eliminated, followed by cyclization and dehydration step to yield <small>L</small>-pyrrolysine.<ref>{{cite journal |title=The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine  |journal = Nature |date=March 31, 2011 |volume=471|issue=7340|pages=647–50|doi=10.1038/nature09918 |pmid= 21455182 |pmc=3070376 |bibcode = 2011Natur.471..647G |last2=Zhang |last3=Green-Church |last4=Krzycki |last1 = Gaston |first1 = Marsha A. }}</ref>

==Catalytic function==
The extra [[pyrroline]] ring is incorporated into the [[active site]] of several [[methyltransferase]]s, where it is believed to rotate relatively freely. It is believed that the ring is involved in positioning and displaying the [[methyl group]] of [[methylamine]] for attack by a [[corrinoid]] [[Cofactor (biochemistry)|cofactor]]. The proposed model is that a nearby [[carboxylic acid]] bearing residue, [[glutamate]], becomes [[protonated]], and the proton can then be transferred to the [[imine]] ring nitrogen, exposing the adjacent ring carbon to [[nucleophilic addition]] by methylamine. The positively charged nitrogen created by this interaction may then interact with the deprotonated glutamate, causing a shift in ring orientation and exposing the methyl group derived from the methylamine to the binding cleft where it can interact with corrinoid. In this way a net {{chem|CH|3|+}} is transferred to the cofactor's [[cobalt]] atom with a change of [[oxidation state]] from +1 to +3. The methylamine-derived [[ammonia]] is then released, restoring the original imine.<ref name=Hao />

==Genetic coding==
Unlike [[posttranslational modification]]s of lysine such as [[hydroxylysine]], [[methyllysine]], and [[hypusine]], pyrrolysine is incorporated during [[translation (genetics)|translation]] ([[protein synthesis]]) as directed by the [[genetic code]], just like the [[standard amino acid]]s. It is encoded in [[mRNA]] by the UAG [[codon]], which in most organisms is the 'amber' [[stop codon]]. This requires only the presence of the ''pylT'' gene, which encodes an unusual [[transfer RNA]] (tRNA) with a CUA anticodon, and the ''[[pylS]]'' gene, which encodes a [[Aminoacyl tRNA synthetases, class II|class II]] [[aminoacyl-tRNA synthetase]] that charges the ''pylT''-derived tRNA with pyrrolysine.

This novel tRNA-aaRS pair ("orthogonal pair") is independent of other synthetases and tRNAs in ''[[Escherichia coli]]'', and further possesses some flexibility in the range of amino acids processed, making it an attractive tool to allow the placement of a possibly wide range of functional [[chemical group]]s at arbitrarily specified locations in modified proteins.<ref>{{cite journal | pmid = 15380192 | doi=10.1016/j.chembiol.2004.07.011 | volume=11 | issue=9 | title=Reactivity and chemical synthesis of <small>L</small>-pyrrolysine – the 22nd genetically encoded amino acid |date=September 2004 | journal= Chemistry & Biology| pages=1317–24 | last1=Hao | first1=B | last2=Zhao | first2=G | last3=Kang | first3=P. T. | last4=Soares | first4=J. A. | last5=Ferguson | first5=T. K. | last6=Gallucci | first6=J | last7=Krzycki | first7=J. A. | last8=Chan | first8=M. K. | doi-access=free }}</ref><ref>{{cite journal | pmid = 19063902 | doi=10.1016/j.jmb.2008.11.032 | volume=385 | issue=4 | title=Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs |date=January 2009 | journal= Journal of Molecular Biology| pages=1156–64  | last1=Li | first1=W. T. | last2=Mahapatra | first2=A | last3=Longstaff | first3=D. G. | last4=Bechtel | first4=J | last5=Zhao | first5=G | last6=Kang | first6=P. T. | last7=Chan | first7=M. K. | last8=Krzycki | first8=J. A. }}</ref> For example, the system provided one of two [[fluorophore]]s incorporated site-specifically within [[calmodulin]] to allow the real-time examination of changes within the protein by [[Förster resonance energy transfer|FRET]] spectroscopy,<ref>{{cite journal | pmid = 19156778 | doi=10.1002/anie.200805420 | volume=48 | issue=9 | title=A pyrrolysine analogue for protein click chemistry | year=2009 | journal= Angewandte Chemie International Edition in English| pages=1633–5 | last1=Fekner | first1=T | last2=Li | first2=X | last3=Lee | first3=M. M. | last4=Chan | first4=M. K. }}</ref> and site-specific introduction of a [[Photolabile protecting group#Photocaging|photocaged]] lysine derivative.<ref>{{cite journal | pmid = 19378306 | doi=10.1002/anie.200900683 | volume=48 | issue=22 | title=A facile system for encoding unnatural amino acids in mammalian cells | pmc=2873846 | year=2009 | journal= Angewandte Chemie International Edition in English| pages=4052–5 | last1=Chen | first1=P. R. | last2=Groff | first2=D | last3=Guo | first3=J | last4=Ou | first4=W | last5=Cellitti | first5=S | last6=Geierstanger | first6=B. H. | last7=Schultz | first7=P. G. }}</ref> ''(See [[Expanded genetic code]])''

It was originally proposed that a specific [[PYLIS downstream sequence|downstream sequence "PYLIS"]], forming a [[stem-loop]] in the [[mRNA]], forced the incorporation of pyrrolysine instead of terminating [[Translation (biology)|translation]] in methanogenic archaea. This would be analogous to the [[SECIS]] element for selenocysteine incorporation.<ref name=Zhang/> However, the PYLIS model has lost favor in view of the lack of structural homology between PYLIS elements and the lack of UAG stops in those species.<ref>{{cite journal|last1=Namy|first1=Olivier|last2=Zhou|first2=Yu|last3=Gundllapalli|first3=Sarath|last4=Polycarpo|first4=Carla R.|last5=Denise|first5=Alain|last6=Rousset|first6=Jean-Pierre|last7=Söll|first7=Dieter|last8=Ambrogelly|first8=Alexandre|title=Adding pyrrolysine to the ''Escherichia coli'' genetic code|journal=[[FEBS Letters]]|date=November 2007|volume=581|issue=27|pages=5282–5288|pmid=17967457|doi=10.1016/j.febslet.2007.10.022|doi-access=free}}</ref>

==Evolution==
The ''pylT'' (tRNA) and ''pylS'' (aa-tRNA synthase) genes are part of an [[operon]] of ''[[Methanosarcina]] barkeri'', with homologues in other sequenced members of the ''Methanosarcinaceae'' family: [[Methanosarcina acetivorans|''M. acetivorans'']], [[Methanosarcina mazei|''M. mazei'']], and [[Methanosarcina thermophila|''M. thermophila'']]. Pyrrolysine-containing proteins are known to include [[monomethylamine methyltransferase]] (mtmB), [[dimethylamine methyltransferase]] (mtbB), and [[trimethylamine methyltransferase]] (mttB). [[Homology (biology)|Homologs]] of ''pylS'' and ''pylT'' have also been found in an Antarctic archaeon, ''[[Methanosarcina barkeri]]'' and a [[Gram-positive]] [[bacterium]], ''[[Desulfitobacterium hafniense]]''.<ref name=Zhang>Reviewed in {{cite journal|title=Pyrrolysine and selenocysteine use dissimilar decoding strategies|journal=Journal of Biological Chemistry|date=May 27, 2005|volume=280|pages=20740–20751|doi=10.1074/jbc.M501458200|pmid=15788401|issue=21|last1=Zhang|first1=Y|last2=Baranov|first2=P. V.|last3=Atkins|first3=J. F.|last4=Gladyshev|first4=V. N.|doi-access=free}}</ref><ref>{{cite journal|title=High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis|journal=Nucleic Acids Research|year=2007|volume=35|pages=4952–4963|issue=15|doi=10.1093/nar/gkm514|pmid=17626042|pmc=1976440|last1=Zhang|first1=Y|last2=Gladyshev|first2=V. N.}}</ref> The other genes of the ''Pyl'' operon mediate pyrrolysine biosynthesis, leading to description of the operon as a "natural genetic code expansion cassette".<ref>{{cite journal|title=A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine|journal=Proceedings of the National Academy of Sciences of the United States of America|date=2007-01-16|volume=104|pages=1021–6|issue=3|doi=10.1073/pnas.0610294104|pmid=17204561|pmc=1783357|bibcode = 2007PNAS..104.1021L |last1=Longstaff|first1=D. G.|last2=Larue|first2=R. C.|last3=Faust|first3=J. E.|last4=Mahapatra|first4=A|last5=Zhang|first5=L|last6=Green-Church|first6=K. B.|last7=Krzycki|first7=J. A.|doi-access=free}}</ref>

A number of evolutionary scenarios have been proposed for the pyrrolysine system. The current (2022) view, given available sequences for tRNA and Pyl-tRNA (PylRS) synthase genes, is that:<ref name=Guo2022>{{cite journal |last1=Guo |first1=LT |last2=Amikura |first2=K |last3=Jiang |first3=HK |last4=Mukai |first4=T |last5=Fu |first5=X |last6=Wang |first6=YS |last7=O'Donoghue |first7=P |last8=Söll |first8=D |last9=Tharp |first9=JM |title=Ancestral archaea expanded the genetic code with pyrrolysine. |journal=The Journal of Biological Chemistry |date=November 2022 |volume=298 |issue=11 |pages=102521 |doi=10.1016/j.jbc.2022.102521 |pmid=36152750|doi-access=free |pmc=9630628 }}</ref>
* tRNA(Pyl) diverged from tRNA(Phe) some time between the divergence of the three domains (~[[last universal common ancestor|LUCA]]) and the divergence of archaeal phyla, but was lost in non-archaeal lineages;<ref name=Guo2022/>
* PylRS originated within a common ancestor of all [[archaea]]. A number of domain organizations of PylRS is known: ''pylS'' itself consists of an [[N-terminal]] tRNA-binding domain and a [[C-terminal]] synthase domain, but other organizations consist of two domains in separate proteins or a protein made up of a lone C-terminal domain. The CTD probably originated from PheRS. The NTD is an archaeal innovation with no known relative. The ancestral PylRS probably adopted the "two separate proteins" configuration.<ref name=Guo2022/>
* The "genetic code expansion cassette" was later transferred into various [[bacteria]]. This cassette's PylRS has a split-domain configuration.<ref name=Guo2022/>

Earlier evolutionary scenarios were limited by the taxonomic range of known synthases:
* In 2007, when use of the amino acid appeared confined to the ''Methanosarcinaceae'', the system was described as a "late archaeal invention" by which a 21st amino acid was added to the genetic code.<ref name=Ambrogelly>{{cite journal|title=Pyrrolysine is not hardwired for cotranslational insertion at UAG codons|journal=Proceedings of the National Academy of Sciences of the United States of America|doi=10.1073/pnas.0611634104|date=2007-02-27|volume=104|pages=3141–3146|issue=9|pmid=17360621|pmc=1805618|bibcode = 2007PNAS..104.3141A |last1=Ambrogelly|first1=A|last2=Gundllapalli|first2=S|last3=Herring|first3=S|last4=Polycarpo|first4=C|last5=Frauer|first5=C|last6=Söll|first6=D|doi-access=free}}</ref> It is now known that a wide range of prokaryotes have these two genes.<ref name=Guo2022/>
* In 2009, structure comparison suggested that PylRS may have originated in the [[last universal common ancestor|LUCA]], but it only persisted in organisms using methylamines as energy sources.<ref name=Kayo>{{cite journal|title=Pyrrolysyl-tRNA synthetase:tRNAPyl structure reveals the molecular basis of orthogonality|journal=Nature|date=2009-02-26|volume=457|pages=1163–1167|doi=10.1038/nature07611|pmc=2648862|pmid=19118381|issue=7233|bibcode = 2009Natur.457.1163N |last1=Nozawa|first1=K|last2=O'Donoghue|first2=P|last3=Gundllapalli|first3=S|last4=Araiso|first4=Y|last5=Ishitani|first5=R|last6=Umehara|first6=T|last7=Söll|first7=D|last8=Nureki|first8=O}}</ref> It is now known that some non-methanogens also have these two genes, but the dating was not too far off.<ref name=Guo2022/>
* In 2009, it was suggested that the system could have migrated into bacteria by [[horizontal gene transfer]].<ref>{{cite book | pmid = 19271184 | doi=10.1007/978-1-60327-853-9_9 | volume=532 | chapter=Horizontal gene transfer and the evolution of methanogenic pathways | year=2009 | pages=163–79 | series=Methods in Molecular Biology | isbn=978-1-60327-852-2 | last1=Fournier | first1=G | title=Horizontal Gene Transfer }}</ref> This is probably true based on the 2022 study, though the paper originally assumed a link to methanogenesis.<ref name=Guo2022/>

==Potential for an alternative translation==
The tRNA(CUA) can be charged with [[lysine]] ''in vitro'' by the concerted action of the ''M. barkeri'' Class I and Class II lysyl-tRNA synthetases, which do not recognize pyrrolysine. Charging a tRNA(CUA) with lysine was originally hypothesized to be the first step in translating UAG amber [[codon]]s as pyrrolysine, a mechanism analogous to that used for [[selenocysteine]]. More recent data favor direct charging of pyrrolysine on to the tRNA(CUA) by the protein product of the ''pylS'' gene, leading to the suggestion that the LysRS1:LysRS2 complex may participate in a parallel pathway designed to ensure that proteins containing the UAG codon can be fully translated using lysine as a substitute amino acid in the event of pyrrolysine deficiency.<ref>{{cite journal|doi=10.1073/pnas.0405362101|pmc=515082|title=An aminoacyl-tRNA synthetase that specifically activates pyrrolysine|pmid=15314242|journal=Proceedings of the National Academy of Sciences of the United States of America|date=2004-08-24|volume=101|issue=34|pages=12450–12454|bibcode = 2004PNAS..10112450P |last1=Polycarpo|first1=C|last2=Ambrogelly|first2=A|last3=Bérubé|first3=A|last4=Winbush|first4=S. M.|last5=McCloskey|first5=J. A.|last6=Crain|first6=P. F.|last7=Wood|first7=J. L.|last8=Söll|first8=D|doi-access=free}}</ref> Further study found that the genes encoding LysRS1 and LysRS2 are not required for normal growth on [[methanol]] and methylamines with normal methyltransferase levels, and they cannot replace ''pylS'' in a recombinant system for UAG amber stop codon suppression.<ref>{{cite journal | pmid = 17542922 | doi=10.1111/j.1365-2958.2007.05740.x | volume=64 | issue=5 | title=Class I and class II lysyl-tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp |date=June 2007 | journal=Molecular Microbiology| pages=1306–18 | last1=Mahapatra | first1=A | last2=Srinivasan | first2=G | last3=Richter | first3=K. B. | last4=Meyer | first4=A | last5=Lienard | first5=T | last6=Zhang | first6=J. K. | last7=Zhao | first7=G | last8=Kang | first8=P. T. | last9=Chan | first9=M | last10=Gottschalk | first10=G | last11=Metcalf | first11=W. W. | last12=Krzycki | first12=J. A. | s2cid=26445329 }}</ref>

==References==
{{reflist}}

==Further reading==
* {{cite journal
 | title = The 22nd Amino Acid
 | year = 2002
 | journal = Science
 | volume = 296
 | issue = 5572
 | pages =1409–1410
 | doi = 10.1126/science.1073339
 | pmid = 12029118 | last1 = Atkins
 | first1 = J. F.
 | last2 = Gesteland
 | first2 = R
 | s2cid = 82054110
 }}
* {{cite journal| title = The direct genetic encoding of pyrrolysine | journal = Current Opinion in Microbiology| volume = 8 | issue = 6 | pages = 706–712 | year = 2005 | doi = 10.1016/j.mib.2005.10.009 | pmid = 16256420| last1 = Krzycki | first1 = J. A. }}

==External links==
* {{cite journal|issn=0009-2347|url=http://pubs.acs.org/cen/topstory/8021/8021notw1.html |journal=Chemical and Engineering News |date= May 27, 2002|volume=80|issue=21|page= 13|title=22nd amino acid identified| first=Amanda | last=Yarnell |doi=10.1021/cen-v080n021.p013}}

{{Amino acids}}

[[Category:Alpha-Amino acids]]
[[Category:Proteinogenic amino acids]]
[[Category:Pyrrolines]]
[[Category:Secondary amino acids]]