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1xrs

From Proteopedia

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Current revision

Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine

Structural highlights

1xrs is a 2 chain structure with sequence from Acetoanaerobium sticklandii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAMD_ACESD Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.,Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15870-5. Epub 2004 Oct 28. PMID:15514022^[3]

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

References

↑ Chang CH, Frey PA. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii. J Biol Chem. 2000 Jan 7;275(1):106-14. PMID:10617592
↑ Tang KH, Chang CH, Frey PA. Electron transfer in the substrate-dependent suicide inactivation of lysine 5,6-aminomutase. Biochemistry. 2001 May 1;40(17):5190-9. PMID:11318641 doi:10.1021/bi010157j
↑ Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15870-5. Epub 2004 Oct 28. PMID:15514022

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xrs"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==
-<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1xrs' size='340' side='right'caption='[[1xrs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetoanaerobium_sticklandii Acetoanaerobium sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [https://pdbe.org/1xrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [https://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KAMDD_CLOSD KAMDD_CLOSD]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref>  [[http://www.uniprot.org/uniprot/KAMED_CLOSD KAMED_CLOSD]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref>
+[https://www.uniprot.org/uniprot/KAMD_ACESD KAMD_ACESD] Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively.<ref>PMID:10617592</ref> <ref>PMID:11318641</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xrs_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xrs_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Aminomutase|Aminomutase]]
+*[[Aminomutase 3D structures|Aminomutase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 12662]]
+[[Category: Acetoanaerobium sticklandii]]
-[[Category: Beta-lysine 5,6-aminomutase]]
+[[Category: Large Structures]]
-[[Category: Behshad, E]]
+[[Category: Behshad E]]
-[[Category: Berkovitch, F]]
+[[Category: Berkovitch F]]
-[[Category: Drennan, C L]]
+[[Category: Drennan CL]]
-[[Category: Enns, E A]]
+[[Category: Enns EA]]
-[[Category: Frey, P A]]
+[[Category: Frey PA]]
-[[Category: Tang, K H]]
+[[Category: Tang KH]]
-[[Category: 5'-deoxyadenosine]]
-[[Category: Adenosylcobalamin]]
-[[Category: B12]]
-[[Category: Cobalamin]]
-[[Category: Conformational change]]
-[[Category: Isomerase]]
-[[Category: Mutase]]
-[[Category: Plp]]
-[[Category: Radical]]
-[[Category: Rossmann domain]]
-[[Category: Tim barrel]]

1xrs

From Proteopedia

Current revision

Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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