This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.


Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


6yme

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:30, 24 January 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6yme' size='340' side='right'caption='[[6yme]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
<StructureSection load='6yme' size='340' side='right'caption='[[6yme]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6yme]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aphha Aphha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YME FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6yme]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aphanothece_halophytica Aphanothece halophytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YME FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glyrA, glyA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=72020 APHHA])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6yme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yme OCA], [https://pdbe.org/6yme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yme RCSB], [https://www.ebi.ac.uk/pdbsum/6yme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yme ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6yme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yme OCA], [https://pdbe.org/6yme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yme RCSB], [https://www.ebi.ac.uk/pdbsum/6yme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yme ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/I7H6W6_APHHA I7H6W6_APHHA]] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051]
+
[https://www.uniprot.org/uniprot/I7H6W6_APHHA I7H6W6_APHHA] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 23: Line 21:
==See Also==
==See Also==
-
*[[Serine hydroxymethyltransferase|Serine hydroxymethyltransferase]]
+
*[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Aphha]]
+
[[Category: Aphanothece halophytica]]
-
[[Category: Glycine hydroxymethyltransferase]]
+
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Angelaccio, S]]
+
[[Category: Angelaccio S]]
-
[[Category: Contestabile, R]]
+
[[Category: Contestabile R]]
-
[[Category: Nogues, I]]
+
[[Category: Nogues I]]
-
[[Category: Ruszkowski, M]]
+
[[Category: Ruszkowski M]]
-
[[Category: Sekula, B]]
+
[[Category: Sekula B]]
-
[[Category: Tramonti, A]]
+
[[Category: Tramonti A]]
-
[[Category: Glycine]]
+
-
[[Category: One-carbon metabolism]]
+
-
[[Category: Plp]]
+
-
[[Category: Serine biosynthesis]]
+
-
[[Category: Tetrahydrofolate]]
+
-
[[Category: Transferase]]
+

Current revision

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-internal aldimine state

PDB ID 6yme

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools