Amino Acids: Difference between revisions

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==22 Standard Amino Acids and Mnemonics==

Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [~~http~~://~~pac~~.iupac.org/publications/pac~~/pdf~~/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.

Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [https://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.

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</tr>

<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. ~~In the early 2000's~~,

<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. Since 2014,

genetically encoded

[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard.

[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard by the World Wide Protein Data Bank<ref name="pdb22" />.

&dagger; Asx: Asn or Asp; Glx: Gln or Glu; Unk: unknown.

[http://~~pac~~.iupac.org/publications/pac~~/pdf~~/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.

[http://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.

</center></td></tr>

</table>

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==L- and D-Amino Acids==

PDB Nomenclature

</td></tr><tr><td>

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</td></tr><tr><td>

ALA ARG ASN ASP CYS GLN GLU HIS ILE LEU LYS MET

PHE PRO SER THR TRP TYR VAL

PHE PRO PYL SEC SER THR TRP TYR VAL

</td><td>

DAL DAR DSG DAS DCY DGN DGL DHI DIL DLE DLY MED

DPN DPR DSN DTH DTR DTY DVA

DPN DPR ?<ref name="ddd">In January, 2022, no D-selenocysteine nor D-pyrrolysine were present in the [[wwPDB]], according to David Armstrong of PDBe.</ref> ?<ref name="ddd" /> DSN DTH DTR DTY DVA

</td></tr></table>

The asymmetric α-carbon in 19 of the standard amino acids (all except glycine) is a chiral center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).

The asymmetric α-carbon in 21 of the standard amino acids (all except glycine) is a chiral (stereogenic) center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).

More than 700 entries in the [[PDB]] contain one or more D amino acids. Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids.

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===Selenocysteine: the 21st amino acid===

Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. ~~Over [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SEC 70~~ entries] in the [[PDB]] include selenocysteine, identified as SEC.

Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. In 2024, over 90 entries in the [[PDB]] include selenocysteine, identified as SEC.

===Pyrrolysine: the 22nd amino acid===

'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, now designated the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [~~http~~://www.rcsb.org/~~pdb/ligand/ligandsummary.do~~?~~hetId~~=~~PYL~~ several entries] in the PDB.

'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, now designated the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text_chem%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_chem_comp_container_identifiers.comp_id%22%2C%22operator%22%3A%22in%22%2C%22negation%22%3Afalse%2C%22value%22%3A%5B%22PYL%22%5D%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22label%22%3A%22text_chem%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22354d8ac467aafef9f60bd804ac85c1b3%22%7D%7D several entries] in the PDB identified as PYL.

See [[Pyrrolysine|more details]].

<!--

Editor's note: Contributions here by [[User:Andrea Gorrell]] were moved to the page on [[Pyrrolysine]].

-->

===No 23rd amino acid?===

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*[[Standard Residues]]

*[http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia]

*[~~http://biochem.ncsu.edu/faculty/mattos/CrystallographyTutorial/AminoAcids.htm The Amino Acids by Paul Swartz~~]

*[[Basics of Protein Structure]]

==References==

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@@ Line 3: / Line 3: @@
 ==22 Standard Amino Acids and Mnemonics==
-Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [http://pac.iupac.org/publications/pac/pdf/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.
+Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [https://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.
 <center>
@@ Line 97: / Line 97: @@
 </tr>
 <tr><td colspan="4"><center>
-<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. In the early 2000's,
+<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. Since 2014,
 genetically encoded
-[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard.
+[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard by the World Wide Protein Data Bank<ref name="pdb22" />.
 <br>
 &dagger; Asx: Asn or Asp; Glx: Gln or Glu; Unk: unknown.
 <br>
-[http://pac.iupac.org/publications/pac/pdf/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.
+[http://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.
 </center></td></tr>
 </table>
@@ Line 123: / Line 123: @@
 ==L- and D-Amino Acids==
-<table border='1' cellpadding='3' align='right' hspace="8"><tr><td colspan='2'>
+<table border='1' cellpadding='3' align='right' hspace="8" class="wikitable" style="margin:0px 0px 0px 8px;"><tr><td colspan='2'>
 PDB Nomenclature
 </td></tr><tr><td>
@@ Line 131: / Line 131: @@
 </td></tr><tr><td>
 ALA<br>ARG<br>ASN<br>ASP<br>CYS<br>GLN<br>GLU<br>HIS<br>ILE<br>LEU<br>LYS<br>MET<br>
-PHE<br>PRO<br>SER<br>THR<br>TRP<br>TYR<br>VAL
+PHE<br>PRO<br>PYL<br>SEC<br>SER<br>THR<br>TRP<br>TYR<br>VAL
 </td><td>
 DAL<br>DAR<br>DSG<br>DAS<br>DCY<br>DGN<br>DGL<br>DHI<br>DIL<br>DLE<br>DLY<br>MED<br>
-DPN<br>DPR<br>DSN<br>DTH<br>DTR<br>DTY<br>DVA
+DPN<br>DPR<br>?<ref name="ddd">In January, 2022, no D-selenocysteine nor D-pyrrolysine were present in the [[wwPDB]], according to David Armstrong of PDBe.</ref><br>?<ref name="ddd" /><br>DSN<br>DTH<br>DTR<br>DTY<br>DVA
 </td></tr></table>
-The asymmetric &alpha;-carbon in 19 of the standard amino acids (all except glycine) is a chiral center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).
+The asymmetric &alpha;-carbon in 21 of the standard amino acids (all except glycine) is a chiral (stereogenic) center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).
 More than 700 entries in the [[PDB]] contain one or more D amino acids. Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids.
@@ Line 147: / Line 147: @@
 ===Selenocysteine: the 21st amino acid===
-Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. Over [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SEC 70 entries] in the [[PDB]] include selenocysteine, identified as SEC.
+Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. In 2024, over 90 entries in the [[PDB]] include selenocysteine, identified as SEC.
 ===Pyrrolysine: the 22nd amino acid===
-'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, now designated the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PYL several entries] in the PDB.
+'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, now designated the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text_chem%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_chem_comp_container_identifiers.comp_id%22%2C%22operator%22%3A%22in%22%2C%22negation%22%3Afalse%2C%22value%22%3A%5B%22PYL%22%5D%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22label%22%3A%22text_chem%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22354d8ac467aafef9f60bd804ac85c1b3%22%7D%7D several entries] in the PDB identified as PYL.
 See [[Pyrrolysine|more details]].
 <!--
 Editor's note: Contributions here by [[User:Andrea Gorrell]] were moved to the page on [[Pyrrolysine]].
 -->
 ===No 23rd amino acid?===
@@ Line 222: / Line 223: @@
 *[[Standard Residues]]
 *[http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia]
-*[http://biochem.ncsu.edu/faculty/mattos/CrystallographyTutorial/AminoAcids.htm The Amino Acids by Paul Swartz]
+*[[Basics of Protein Structure]]
 ==References==
 <references />