1lc3: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1lc3.jpg|left|200px]]


{{Structure
==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==
|PDB= 1lc3 |SIZE=350|CAPTION= <scene name='initialview01'>1lc3</scene>, resolution 1.50&Aring;
<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
<table><tr><td colspan='2'>[[1lc3]] is a 1 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=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [https://pdbe.org/1lc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1lc0|1LC0]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
 
== Evolutionary Conservation ==
'''Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lc/1lc3_consurf.spt"</scriptWhenChecked>
Biliverdin reductase (BVR) catalyzes the last step in heme degradation by reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IXalpha, to bilirubin with the concomitant oxidation of a beta-nicotinamide adenine dinucleotide (NADH) or beta-nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. Bilirubin is the major bile pigment in mammals and has antioxidant and anticompliment activity. We have determined X-ray crystal structures of apo rat BVR and its complex with NADH at 1.2 A and 1.5 A resolution, respectively. In agreement with an independent structure determination of the apo-enzyme, BVR consists of an N-terminal dinucleotide-binding domain (Rossmann-fold) and a C-terminal domain that contains a six-stranded beta-sheet that is flanked on one face by several alpha-helices. The C-terminal and N-terminal domains interact extensively, forming the active site cleft at their interface. The cofactor complex structure reported here reveals that the cofactor nicotinamide ring extends into the active site cleft, where it is adjacent to conserved amino acid residues and, consistent with the known stereochemistry of the reaction catalyzed by BVR, the si face of the ring is accessible for hydride transfer. The only titratable side-chain that appears to be suitably positioned to function as a general acid in catalysis is Tyr97. This residue, however, is not essential for catalysis, since the Tyr97Phe mutant protein retains 50% activity. This finding suggests that the dominant role in catalysis may be performed by hydride transfer from the cofactor, a process that may be promoted by proximity of the invariant residues Glu96, Glu123, and Glu126, to the nicotinamide ring.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1LC3 is a [[Single protein]] structure of sequence 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=1LC3 OCA].  
</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=1lc3 ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex., Whitby FG, Phillips JD, Hill CP, McCoubrey W, Maines MD, J Mol Biol. 2002 Jun 21;319(5):1199-210. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12079357 12079357]
</StructureSection>
[[Category: Biliverdin reductase]]
[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
[[Category: Single protein]]
[[Category: Hill CP]]
[[Category: Hill, C P.]]
[[Category: Maines MD]]
[[Category: Maines, M D.]]
[[Category: McCoubrey W]]
[[Category: McCoubrey, W.]]
[[Category: Phillips JD]]
[[Category: Phillips, J D.]]
[[Category: Whitby FG]]
[[Category: Whitby, F G.]]
[[Category: bile pigment]]
[[Category: bilirubin]]
[[Category: biliverdin reductase]]
[[Category: heme]]
[[Category: nadh]]
[[Category: tetrapyrrole]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:00:56 2008''

Latest revision as of 10:31, 14 February 2024

Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor ComplexCrystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex

Structural highlights

1lc3 is a 1 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 1.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BIEA_RAT Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.

Evolutionary Conservation

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

1lc3, resolution 1.50Å

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=1lc3&oldid=4050623"