4m51

From Proteopedia

(Difference between revisions)

Revision as of 10:56, 21 December 2022

Crystal structure of amidohydrolase nis_0429 (ser145ala mutant) from nitratiruptor sp. sb155-2

Structural highlights

4m51 is a 1 chain structure with sequence from Nitratiruptor sp. SB155-2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MQNX_NITSB Catalyzes the deamination of aminodeoxyfutalosine (AFL) into futalosine (FL), a step in the biosynthesis of menaquinone (MK, vitamin K2). To a lesser extent, can also deaminate 5'-methylthioadenosine.^[1]

Publication Abstract from PubMed

Proteins of unknown function belonging to cog1816 and cog0402 were characterized. Sav2595 from Steptomyces avermitilis MA-4680, Acel0264 from Acidothermus cellulolyticus 11B, Nis0429 from Nitratiruptor sp. SB155-2 and Dr0824 from Deinococcus radiodurans R1 were cloned, purified, and their substrate profiles determined. These enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. It was shown here that these enzymes actually deaminate 6-aminodeoxyfutalosine. The deamination of 6-aminodeoxyfutalosine is part of an alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminodeoxyfutalosine is deaminated by these enzymes with catalytic efficiencies greater than 10(5) M(-1) s(-1), Km values of 0.9-6.0 muM, and kcat values of 1.2-8.6 s(-1). Adenosine, 2'-deoxyadenosine, thiomethyladenosine, and S-adenosylhomocysteine are deaminated at least an order of magnitude slower than 6-aminodeoxyfutalosine. The crystal structure of Nis0429 was determined and the substrate, 6-aminodeoxyfutalosine, was positioned in the active site on the basis of the presence of adventitiously bound benzoic acid. In this model, Ser-145 interacts with the carboxylate moiety of the substrate. The structure of Dr0824 was also determined, but a collapsed active site pocket prevented docking of substrates. A computational model of Sav2595 was built on the basis of the crystal structure of adenosine deaminase and substrates were docked. The model predicted a conserved arginine after beta-strand 1 to be partially responsible for the substrate specificity of Sav2595.

Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.,Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM Biochemistry. 2013 Sep 17;52(37):6525-36. doi: 10.1021/bi400750a. Epub 2013 Sep, 4. PMID:23972005^[2]

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

References

↑ Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17;52(37):6525-36. doi: 10.1021/bi400750a. Epub 2013 Sep, 4. PMID:23972005 doi:10.1021/bi400750a
↑ Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17;52(37):6525-36. doi: 10.1021/bi400750a. Epub 2013 Sep, 4. PMID:23972005 doi:10.1021/bi400750a

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4m51"

@@ Line 1: / Line 1: @@
 ==Crystal structure of amidohydrolase nis_0429 (ser145ala mutant) from nitratiruptor sp. sb155-2==
-<StructureSection load='4m51' size='340' side='right' caption='[[4m51]], [[Resolution|resolution]] 1.08&Aring;' scene=''>
+<StructureSection load='4m51' size='340' side='right'caption='[[4m51]], [[Resolution|resolution]] 1.08&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4m51]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nitsb Nitsb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M51 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M51 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4m51]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nitratiruptor_sp._SB155-2 Nitratiruptor sp. SB155-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M51 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3v7p|3v7p]]</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=4m51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m51 OCA], [https://pdbe.org/4m51 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m51 RCSB], [https://www.ebi.ac.uk/pdbsum/4m51 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m51 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NIS_0429 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=387092 NITSB])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4m51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m51 OCA], [http://pdbe.org/4m51 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m51 RCSB], [http://www.ebi.ac.uk/pdbsum/4m51 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m51 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MQNX_NITSB MQNX_NITSB]] Catalyzes the deamination of aminodeoxyfutalosine (AFL) into futalosine (FL), a step in the biosynthesis of menaquinone (MK, vitamin K2). To a lesser extent, can also deaminate 5'-methylthioadenosine.<ref>PMID:23972005</ref>
+[https://www.uniprot.org/uniprot/MQNX_NITSB MQNX_NITSB] Catalyzes the deamination of aminodeoxyfutalosine (AFL) into futalosine (FL), a step in the biosynthesis of menaquinone (MK, vitamin K2). To a lesser extent, can also deaminate 5'-methylthioadenosine.<ref>PMID:23972005</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Nitsb]]
+[[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Nitratiruptor sp. SB155-2]]
-[[Category: EFI, Enzyme Function Initiative]]
+[[Category: Almo SC]]
-[[Category: Gobble, A]]
+[[Category: Gobble A]]
-[[Category: Patskovsky, Y]]
+[[Category: Patskovsky Y]]
-[[Category: Raushel, F M]]
+[[Category: Raushel FM]]
-[[Category: Toro, R]]
+[[Category: Toro R]]
-[[Category: Amidohydrolase]]
-[[Category: Efi]]
-[[Category: Enzyme function initiative]]
-[[Category: Hydrolase]]
-[[Category: Iron binding site]]

4m51

From Proteopedia

Revision as of 10:56, 21 December 2022

Crystal structure of amidohydrolase nis_0429 (ser145ala mutant) from nitratiruptor sp. sb155-2

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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