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3kp0

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Revision as of 08:57, 26 December 2018

Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with 2,4-diaminobutyrate (DAB) (Aerobic)

Structural highlights

3kp0 is a 8 chain structure with sequence from Acest. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3kow, 3kox, 3koy, 3koz, 3kp1
Gene:	oraE (ACEST), oraS (ACEST)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[OAME_CLOSD] Component of a complex that catalyzes the reversible migration of the omega amino group of D-ornithine to C-4 to form (2R,4S)-2,4-diaminopentanoic acid. OraE may be the catalytic subunit. Active only on D-ornithine and 2,4-diaminopentanoic acid but not active on L-ornithine, L-beta-lysine, L-alpha-lysine or D-alpha-lysine.^[1] ^[2] ^[3] [OAMS_CLOSD] Component of a complex that catalyzes the reversible migration of the omega amino group of D-ornithine to C-4 to form (2R,4S)-2,4-diaminopentanoic acid. The role of OraS remains obscure; however, it seems to be required for a correct folding of the OraE subunit. The complex is active only on D-ornithine and 2,4-diaminopentanoic acid and not active on L-ornithine, L-beta-lysine, L-alpha-lysine or D-alpha-lysine.^[4] ^[5] ^[6]

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

D-ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin (AdoCbl) to a pyridoxal 5'-phosphate (PLP) cofactor. We have solved OAM crystal structures in different catalytic states that together demonstrate unusual stability of the AdoCbl Co-C bond and that radical catalysis is coupled to large-scale domain motion. The 2.0-A substrate-free enzyme crystal structure reveals the Rossmann domain, harboring the intact AdoCbl cofactor, is tilted toward the edge of the PLP binding triose-phosphate isomerase barrel domain. The PLP forms an internal aldimine link to the Rossmann domain through Lys(629), effectively locking the enzyme in this "open" pre-catalytic conformation. The distance between PLP and 5'-deoxyadenosyl group is 23 A, and large-scale domain movement is thus required prior to radical catalysis. The OAM crystals contain two Rossmann domains within the asymmetric unit that are unconstrained by the crystal lattice. Surprisingly, the binding of various ligands to OAM crystals (in an oxygen-free environment) leads to transimination in the absence of significant reorientation of the Rossmann domains. In contrast, when performed under aerobic conditions, this leads to extreme disorder in the latter domains correlated with the loss of the 5'-deoxyadenosyl group. Our data indicate turnover and hence formation of the "closed" conformation is occurring within OAM crystals, but that the equilibrium is poised toward the open conformation. We propose that substrate binding induces large-scale domain motion concomitant with a reconfiguration of the 5'-deoxyadenosyl group, triggering radical catalysis in OAM.

Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.,Wolthers KR, Levy C, Scrutton NS, Leys D J Biol Chem. 2010 Apr 30;285(18):13942-50. Epub 2010 Jan 27. PMID:20106986^[7]

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

References

↑ Chen HP, Wu SH, Lin YL, Chen CM, Tsay SS. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-ornithine aminomutase from Clostridium sticklandii. J Biol Chem. 2001 Nov 30;276(48):44744-50. Epub 2001 Sep 27. PMID:11577113 doi:http://dx.doi.org/10.1074/jbc.M108365200
↑ Somack R, Costilow RN. Purification and properties of a pyridoxal phosphate and coenzyme B 12 dependent D- -ornithine 5,4-aminomutase. Biochemistry. 1973 Jul 3;12(14):2597-604. PMID:4711468
↑ Chen HP, Wu SH, Lin YL, Chen CM, Tsay SS. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-ornithine aminomutase from Clostridium sticklandii. J Biol Chem. 2001 Nov 30;276(48):44744-50. Epub 2001 Sep 27. PMID:11577113 doi:http://dx.doi.org/10.1074/jbc.M108365200
↑ Chen HP, Wu SH, Lin YL, Chen CM, Tsay SS. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-ornithine aminomutase from Clostridium sticklandii. J Biol Chem. 2001 Nov 30;276(48):44744-50. Epub 2001 Sep 27. PMID:11577113 doi:http://dx.doi.org/10.1074/jbc.M108365200
↑ Somack R, Costilow RN. Purification and properties of a pyridoxal phosphate and coenzyme B 12 dependent D- -ornithine 5,4-aminomutase. Biochemistry. 1973 Jul 3;12(14):2597-604. PMID:4711468
↑ Somack R, Costilow RN. Purification and properties of a pyridoxal phosphate and coenzyme B 12 dependent D- -ornithine 5,4-aminomutase. Biochemistry. 1973 Jul 3;12(14):2597-604. PMID:4711468
↑ Wolthers KR, Levy C, Scrutton NS, Leys D. Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. J Biol Chem. 2010 Apr 30;285(18):13942-50. Epub 2010 Jan 27. PMID:20106986 doi:10.1074/jbc.M109.068908

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/3kp0"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with 2,4-diaminobutyrate (DAB) (Aerobic)==
 <StructureSection load='3kp0' size='340' side='right' caption='[[3kp0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kp0]] is a 8 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=3KP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KP0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kp0]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Acest Acest]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KP0 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=Z98:(2S)-2-AMINO-4-{[(1Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUTANOIC+ACID'>Z98</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kow|3kow]], [[3kox|3kox]], [[3koy|3koy]], [[3koz|3koz]], [[3kp1|3kp1]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oraE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662]), oraS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oraE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ACEST]), oraS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ACEST])</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=3kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp0 OCA], [http://pdbe.org/3kp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kp0 RCSB], [http://www.ebi.ac.uk/pdbsum/3kp0 PDBsum]</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=3kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp0 OCA], [http://pdbe.org/3kp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kp0 RCSB], [http://www.ebi.ac.uk/pdbsum/3kp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kp0 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kp0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kp0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 36: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 12662]]
+[[Category: Acest]]
 [[Category: Levy, C W]]
 [[Category: Leys, D]]

3kp0

From Proteopedia

Revision as of 08:57, 26 December 2018

Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with 2,4-diaminobutyrate (DAB) (Aerobic)

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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