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.


1gyj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:25, 27 March 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1gyj.jpg|left|200px]]
 
-
{{Structure
+
==The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity==
-
|PDB= 1gyj |SIZE=350|CAPTION= <scene name='initialview01'>1gyj</scene>, resolution 2.1&Aring;
+
<StructureSection load='1gyj' size='340' side='right'caption='[[1gyj]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<table><tr><td colspan='2'>[[1gyj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYJ FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylpyruvate_tautomerase Phenylpyruvate tautomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.2.1 5.3.2.1] </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]] 2.1&#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=1gyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyj OCA], [https://pdbe.org/1gyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyj RCSB], [https://www.ebi.ac.uk/pdbsum/1gyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyj ProSAT]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyj OCA], [http://www.ebi.ac.uk/pdbsum/1gyj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gyj RCSB]</span>
+
[https://www.uniprot.org/uniprot/PPTA_ECOLI PPTA_ECOLI] Can use enol isomers of phenylpyruvate, 2-hydroxy-2,4-pentadienoate and (p-hydroxyphenyl)pyruvate as substrates.<ref>PMID:12356301</ref>
-
}}
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
'''THE CRYSTAL STRUCTURE OF YDCE, A 4-OXALOCROTONATE TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR OLIGOMER DIVERSITY'''
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyj_consurf.spt"</scriptWhenChecked>
-
==Overview==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
The tautomerase superfamily consists of three major families represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), and macrophage migration inhibitory factor (MIF). The members of this superfamily are structurally homologous proteins constructed from a simple beta-alpha-beta fold that share a key mechanistic feature; they use an amino-terminal proline, which has an unusually low pK(a), as the general base in a keto-enol tautomerization. Several new members of the 4-OT family have now been identified using PSI-BLAST and categorized into five subfamilies on the basis of multiple-sequence alignments and the conservation of key catalytic and structural residues. The members of subfamily 5, which includes a hypothetical protein designated YdcE from Escherichia coli, are predicted not to form hexamers. The crystal structure of YdcE has been determined to 1.35 A resolution and confirms that it is a dimer. In addition, YdcE complexed with (E)-2-fluoro-p-hydroxycinnamate, identified as a potent competitive inhibitor of this enzyme, as well as N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) and benzoate are also presented. These latter crystal structures reveal the location of the active site and suggest a mechanism for the observed YdcE-catalyzed tautomerization reaction. The dimeric arrangement of YdcE represents a new structure in the 4-OT family and demonstrates structural diversity within the 4-OT family not previously reported.
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==About this Structure==
+
</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=1gyj ConSurf].
-
1GYJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYJ OCA].
+
<div style="clear:both"></div>
-
 
+
== References ==
-
==Reference==
+
<references/>
-
The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity., Almrud JJ, Kern AD, Wang SC, Czerwinski RM, Johnson WH Jr, Murzin AG, Hackert ML, Whitman CP, Biochemistry. 2002 Oct 8;41(40):12010-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12356301 12356301]
+
__TOC__
-
[[Category: Escherichia coli]]
+
</StructureSection>
-
[[Category: Phenylpyruvate tautomerase]]
+
[[Category: Escherichia coli K-12]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Almrud, J.]]
+
[[Category: Almrud J]]
-
[[Category: Czerwinski, R.]]
+
[[Category: Czerwinski R]]
-
[[Category: Hackert, M.]]
+
[[Category: Hackert M]]
-
[[Category: Johnson, W.]]
+
[[Category: Johnson W]]
-
[[Category: Kern, A.]]
+
[[Category: Kern A]]
-
[[Category: Murzin, A.]]
+
[[Category: Murzin A]]
-
[[Category: Wang, S.]]
+
[[Category: Wang S]]
-
[[Category: Whitman, C.]]
+
[[Category: Whitman C]]
-
[[Category: tautomerase,isomerase,hypothetical protein,complete proteome]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:54:12 2008''
+

Current revision

The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity

PDB ID 1gyj

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/1gyj"
Personal tools