5err: Difference between revisions

Latest revision as of 08:19, 12 July 2023

GephE in complex with Mg(2+) - ADP

Structural highlights

5err is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:	ACT, ADP, MG, MPD, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GEPH_RAT Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.^[1] ^[2]

Publication Abstract from PubMed

The molybdenum cofactor (Moco) is essential for the catalytic activity of all molybdenum-containing enzymes with the exception of nitrogenase. Moco biosynthesis follows an evolutionarily highly conserved pathway and genetic deficiencies in the corresponding human enzymes result in Moco deficiency, which manifests itself in severe neurological symptoms and death in childhood. In humans the final steps of Moco biosynthesis are catalyzed by gephyrin, specifically the penultimate adenylation of molybdopterin (MPT) by its N-terminal G domain (GephG) and the final metal incorporation by its C-terminal E domain (GephE). To better understand the poorly defined molecular framework of this final step, we determined high-resolution crystal structures of GephE in the apo state and in complex with ADP, AMP, and molybdate. Our data provide novel insights into the catalytic steps leading to final Moco maturation, namely deadenylation as well as molybdate binding and insertion.

Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis.,Kasaragod VB, Schindelin H Structure. 2016 May 3;24(5):782-8. doi: 10.1016/j.str.2016.02.023. Epub 2016 Apr , 21. PMID:27112598^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kirsch J, Wolters I, Triller A, Betz H. Gephyrin antisense oligonucleotides prevent glycine receptor clustering in spinal neurons. Nature. 1993 Dec 23-30;366(6457):745-8. PMID:8264797 doi:https://dx.doi.org/10.1038/366745a0
↑ Stallmeyer B, Schwarz G, Schulze J, Nerlich A, Reiss J, Kirsch J, Mendel RR. The neurotransmitter receptor-anchoring protein gephyrin reconstitutes molybdenum cofactor biosynthesis in bacteria, plants, and mammalian cells. Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1333-8. PMID:9990024
↑ Kasaragod VB, Schindelin H. Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Structure. 2016 May 3;24(5):782-8. doi: 10.1016/j.str.2016.02.023. Epub 2016 Apr , 21. PMID:27112598 doi:https://dx.doi.org/10.1016/j.str.2016.02.023

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kirsch J, Wolters I, Triller A, Betz H. Gephyrin antisense oligonucleotides prevent glycine receptor clustering in spinal neurons. Nature. 1993 Dec 23-30;366(6457):745-8. PMID:8264797 doi:https://dx.doi.org/10.1038/366745a0

[2] Stallmeyer B, Schwarz G, Schulze J, Nerlich A, Reiss J, Kirsch J, Mendel RR. The neurotransmitter receptor-anchoring protein gephyrin reconstitutes molybdenum cofactor biosynthesis in bacteria, plants, and mammalian cells. Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1333-8. PMID:9990024

[3] Kasaragod VB, Schindelin H. Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Structure. 2016 May 3;24(5):782-8. doi: 10.1016/j.str.2016.02.023. Epub 2016 Apr , 21. PMID:27112598 doi:https://dx.doi.org/10.1016/j.str.2016.02.023

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='5err' size='340' side='right'caption='[[5err]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5err]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ERR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ERR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5err]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ERR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ERR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.65&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Gphn, Gph ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5err FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5err OCA], [http://pdbe.org/5err PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5err RCSB], [http://www.ebi.ac.uk/pdbsum/5err PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5err 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=5err FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5err OCA], [https://pdbe.org/5err PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5err RCSB], [https://www.ebi.ac.uk/pdbsum/5err PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5err ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GEPH_RAT GEPH_RAT]] Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.<ref>PMID:8264797</ref> <ref>PMID:9990024</ref>
+[https://www.uniprot.org/uniprot/GEPH_RAT GEPH_RAT] Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.<ref>PMID:8264797</ref> <ref>PMID:9990024</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Kasaragod, V B]]
+[[Category: Rattus norvegicus]]
-[[Category: Schindelin, H]]
+[[Category: Kasaragod VB]]
-[[Category: Moco]]
+[[Category: Schindelin H]]
-[[Category: Molybdenum and tungsten cofactor]]
-[[Category: Terminal step]]
-[[Category: Transferase]]
-[[Category: Wco]]

5err: Difference between revisions

Latest revision as of 08:19, 12 July 2023

GephE in complex with Mg(2+) - ADP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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