1tb3: Difference between revisions

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[[Image:1tb3.png|left|200px]]


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==Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase==
The line below this paragraph, containing "STRUCTURE_1tb3", creates the "Structure Box" on the page.
<StructureSection load='1tb3' size='340' side='right'caption='[[1tb3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1tb3]] is a 8 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=1TB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TB3 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
{{STRUCTURE_1tb3|  PDB=1tb3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tb3 OCA], [https://pdbe.org/1tb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tb3 RCSB], [https://www.ebi.ac.uk/pdbsum/1tb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tb3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HAOX2_RAT HAOX2_RAT] Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.
== 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/tb/1tb3_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=1tb3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Long chain hydroxy acid oxidase (LCHAO) is a member of an FMN-dependent enzyme family that oxidizes L-2-hydroxy acids to ketoacids. LCHAO is a peroxisomal enzyme, and the identity of its physiological substrate is unclear. Mandelate is the most efficient substrate known and is commonly used in the test tube. LCHAO differs from most family members in that one of the otherwise invariant active site residues is a phenylalanine (Phe23) instead of a tyrosine. We now report the crystal structure of LCHAO. It shows the same beta8alpha8 TIM barrel structure as other structurally characterized family members, e.g., spinach glycolate oxidase (GOX) and the electron transferases yeast flavocytochrome b2 (FCB2) and Pseudomonas putida mandelate dehydrogenase (MDH). Loop 4, which is mobile in other family members, is visible in part. An acetate ion is present in the active site. The flavin interacts with the protein in the same way as in the electron transferases, and not as in GOX, an unexpected observation. An interpretation is proposed to explain this difference between GOX on one hand and FCB2 and LCHAO on the other hand, which had been proposed to arise from the differences between family members in their reactivity with oxygen. A comparison of models of the substrate bound to various published structures suggests that the very different reactivity with mandelate of LCHAO, GOX, FCB2, and MDH cannot be rationalized by a hydride transfer mechanism.


===Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase===
Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase.,Cunane LM, Barton JD, Chen ZW, Le KH, Amar D, Lederer F, Mathews FS Biochemistry. 2005 Feb 8;44(5):1521-31. PMID:15683236<ref>PMID:15683236</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1tb3" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_15683236}}, adds the Publication Abstract to the page
*[[Glycolate oxidase 3D structures|Glycolate oxidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 15683236 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15683236}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1TB3 is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TB3 OCA].
 
==Reference==
<ref group="xtra">PMID:15683236</ref><ref group="xtra">PMID:2681790</ref><ref group="xtra">PMID:2329585</ref><references group="xtra"/>
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
[[Category: Amar, D.]]
[[Category: Amar D]]
[[Category: Barton, J D.]]
[[Category: Barton JD]]
[[Category: Chen, Z W.]]
[[Category: Chen ZW]]
[[Category: Cunane, L M.]]
[[Category: Cunane LM]]
[[Category: Le, K H.D.]]
[[Category: Le KHD]]
[[Category: Lederer, F.]]
[[Category: Lederer F]]
[[Category: Mathews, F S.]]
[[Category: Mathews FS]]
[[Category: Flavoprotein]]
[[Category: Long chain alpha-hydroxy acid oxidase]]
[[Category: Oxidase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:36:53 2009''

Latest revision as of 09:28, 23 August 2023

Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid OxidaseCrystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase

Structural highlights

1tb3 is a 8 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 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HAOX2_RAT Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.

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

Long chain hydroxy acid oxidase (LCHAO) is a member of an FMN-dependent enzyme family that oxidizes L-2-hydroxy acids to ketoacids. LCHAO is a peroxisomal enzyme, and the identity of its physiological substrate is unclear. Mandelate is the most efficient substrate known and is commonly used in the test tube. LCHAO differs from most family members in that one of the otherwise invariant active site residues is a phenylalanine (Phe23) instead of a tyrosine. We now report the crystal structure of LCHAO. It shows the same beta8alpha8 TIM barrel structure as other structurally characterized family members, e.g., spinach glycolate oxidase (GOX) and the electron transferases yeast flavocytochrome b2 (FCB2) and Pseudomonas putida mandelate dehydrogenase (MDH). Loop 4, which is mobile in other family members, is visible in part. An acetate ion is present in the active site. The flavin interacts with the protein in the same way as in the electron transferases, and not as in GOX, an unexpected observation. An interpretation is proposed to explain this difference between GOX on one hand and FCB2 and LCHAO on the other hand, which had been proposed to arise from the differences between family members in their reactivity with oxygen. A comparison of models of the substrate bound to various published structures suggests that the very different reactivity with mandelate of LCHAO, GOX, FCB2, and MDH cannot be rationalized by a hydride transfer mechanism.

Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase.,Cunane LM, Barton JD, Chen ZW, Le KH, Amar D, Lederer F, Mathews FS Biochemistry. 2005 Feb 8;44(5):1521-31. PMID:15683236[1]

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

See Also

References

  1. Cunane LM, Barton JD, Chen ZW, Le KH, Amar D, Lederer F, Mathews FS. Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase. Biochemistry. 2005 Feb 8;44(5):1521-31. PMID:15683236 doi:10.1021/bi048616e

1tb3, resolution 2.30Å

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