1c0l: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1c0l.jpg|left|200px]]


{{Structure
==D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION==
|PDB= 1c0l |SIZE=350|CAPTION= <scene name='initialview01'>1c0l</scene>, resolution 1.73&Aring;
<StructureSection load='1c0l' size='340' side='right'caption='[[1c0l]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FLA:TRIFLUOROALANINE'>FLA</scene>
<table><tr><td colspan='2'>[[1c0l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0L FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.73&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FLA:TRIFLUOROALANINE'>FLA</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0l OCA], [https://pdbe.org/1c0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0l RCSB], [https://www.ebi.ac.uk/pdbsum/1c0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0l ProSAT]</span></td></tr>
|RELATEDENTRY=[[1c0i|1C0I]], [[1c0k|1C0K]], [[1c0p|1C0P]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1c0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0l OCA], [http://www.ebi.ac.uk/pdbsum/1c0l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1c0l RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
== 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/c0/1c0l_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1c0l ConSurf].
<div style="clear:both"></div>


'''D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION'''
==See Also==
 
*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.
[[Category: Large Structures]]
 
[[Category: Rhodotorula toruloides]]
==About this Structure==
[[Category: Diederichs K]]
1C0L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0L OCA].
[[Category: Ghisla S]]
 
[[Category: Molla G]]
==Reference==
[[Category: Pilone MS]]
The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation., Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S, Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11070076 11070076]
[[Category: Umhau S]]
[[Category: Rhodosporidium toruloides]]
[[Category: Welte W]]
[[Category: Single protein]]
[[Category: Diederichs, K.]]
[[Category: Ghisla, S.]]
[[Category: Molla, G.]]
[[Category: Pilone, M S.]]
[[Category: Umhau, S.]]
[[Category: Welte, W.]]
[[Category: flavin containing protein alpha-beta-alpha motif]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:12:11 2008''

Latest revision as of 09:40, 7 February 2024

D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATIOND-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION

Structural highlights

1c0l is a 1 chain structure with sequence from Rhodotorula toruloides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.73Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OXDA_RHOTO This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.

Evolutionary Conservation

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

See Also

1c0l, resolution 1.73Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1c0l&oldid=4040903"