This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1pwe

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:11, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1pwe.gif|left|200px]]
 
-
{{Structure
+
==Rat Liver L-Serine Dehydratase Apo Enzyme==
-
|PDB= 1pwe |SIZE=350|CAPTION= <scene name='initialview01'>1pwe</scene>, resolution 2.80&Aring;
+
<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<table><tr><td colspan='2'>[[1pwe]] is a 6 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=1PWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17]
+
</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>
-
|GENE=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [https://pdbe.org/1pwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [https://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe ProSAT]</span></td></tr>
-
}}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SDHL_RAT SDHL_RAT]
 +
== 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/pw/1pwe_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=1pwe ConSurf].
 +
<div style="clear:both"></div>
-
'''Rat Liver L-Serine Dehydratase Apo Enzyme'''
+
==See Also==
-
 
+
*[[Deaminase 3D structures|Deaminase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent dehydration of L-serine to yield pyruvate and ammonia. Liver SDH plays an important role in gluconeogenesis. Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group of serine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatic hydrolysis to produce pyruvate. The crystal structure of rat liver apo-SDH was determined by single isomorphous replacement at 2.8 A resolution. The holo-SDH crystallized with O-methylserine (OMS) was also determined at 2.6 A resolution by molecular replacement. SDH is composed of two domains, and each domain has a typical alphabeta-open structure. The active site is located in the cleft between the two domains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can form the Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimer by inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed. Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization does not close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence ((168)GGGGL(172)) and forms hydrogen bonds with the amide groups of those amino acid residues, suggesting that the phosphate group can be protonated. N(1) of PLP participates in a hydrogen bond with Cys303, and similar hydrogen bonds with N(1) participating are seen in other beta-elimination enzymes. These hydrogen bonding schemes indicate that N(1) is not protonated, and thus, the pyridine ring cannot take a quinone-like structure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by forming the resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalytic mechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a general acid to donate a proton to the leaving hydroxyl group of serine.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1PWE 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=1PWE OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of serine dehydratase from rat liver., Yamada T, Komoto J, Takata Y, Ogawa H, Pitot HC, Takusagawa F, Biochemistry. 2003 Nov 11;42(44):12854-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14596599 14596599]
+
-
[[Category: L-serine ammonia-lyase]]
+
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
-
[[Category: Single protein]]
+
[[Category: Komoto J]]
-
[[Category: Komoto, J.]]
+
[[Category: Ogawa H]]
-
[[Category: Ogawa, H.]]
+
[[Category: Takata Y]]
-
[[Category: Takata, Y.]]
+
[[Category: Takusagawa F]]
-
[[Category: Takusagawa, F.]]
+
[[Category: Yamada T]]
-
[[Category: Yamada, T.]]
+
-
[[Category: apo enzyme]]
+
-
[[Category: l-serine dehydratase]]
+
-
[[Category: rat liver]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:29:51 2008''
+

Current revision

Rat Liver L-Serine Dehydratase Apo Enzyme

PDB ID 1pwe

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pwe"
Personal tools