1gde

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (23:30, 27 December 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1gde.jpg|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM==
-
|PDB= 1gde |SIZE=350|CAPTION= <scene name='initialview01'>1gde</scene>, resolution 1.8&Aring;
+
<StructureSection load='1gde' size='340' side='right'caption='[[1gde]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene> and <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene>
+
<table><tr><td colspan='2'>[[1gde]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDE 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]] 1.8&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gde OCA], [https://pdbe.org/1gde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gde RCSB], [https://www.ebi.ac.uk/pdbsum/1gde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gde ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/O59096_PYRHO O59096_PYRHO]
 +
== 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/gd/1gde_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=1gde ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We determined the crystal structure of the liganded form of alpha-aminotransferase from a hyperthermophile, Pyrococcus horikoshii. This hyperthermophilic enzyme did not show domain movement upon binding of an acidic substrate, glutamate, except for a small movement of the alpha-helix from Glu16 to Ala25. The omega-carboxyl group of the acidic substrate was recognized by Tyr70* without its side-chain movement, but not by positively charged Arg or Lys. Compared with the homologous enzymes from Thermus thermophilus HB8 and Escherichia coli, it was suggested that the more thermophilic the enzyme is, the smaller the domain movement is. This rule seems to be applicable to many other enzymes already reported.
-
'''CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM'''
+
Temperature dependence of the enzyme-substrate recognition mechanism.,Ura H, Harata K, Matsui I, Kuramitsu S J Biochem. 2001 Jan;129(1):173-8. PMID:11134972<ref>PMID:11134972</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1gde" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
We determined the crystal structure of the liganded form of alpha-aminotransferase from a hyperthermophile, Pyrococcus horikoshii. This hyperthermophilic enzyme did not show domain movement upon binding of an acidic substrate, glutamate, except for a small movement of the alpha-helix from Glu16 to Ala25. The omega-carboxyl group of the acidic substrate was recognized by Tyr70* without its side-chain movement, but not by positively charged Arg or Lys. Compared with the homologous enzymes from Thermus thermophilus HB8 and Escherichia coli, it was suggested that the more thermophilic the enzyme is, the smaller the domain movement is. This rule seems to be applicable to many other enzymes already reported.
+
*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1GDE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDE OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Large Structures]]
-
Temperature dependence of the enzyme-substrate recognition mechanism., Ura H, Harata K, Matsui I, Kuramitsu S, J Biochem. 2001 Jan;129(1):173-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11134972 11134972]
+
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
-
[[Category: Single protein]]
+
[[Category: Harata K]]
-
[[Category: Harata, K.]]
+
[[Category: Kuramitsu S]]
-
[[Category: Kuramitsu, S.]]
+
[[Category: Matsui I]]
-
[[Category: Matsui, I.]]
+
[[Category: Ura H]]
-
[[Category: Ura, H.]]
+
-
[[Category: GLU]]
+
-
[[Category: PLP]]
+
-
[[Category: aminotransferase]]
+
-
[[Category: pyridoxal enzyme]]
+
-
[[Category: temperature dependence of substrate recognition]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:21:37 2008''
+

Current revision

CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM

PDB ID 1gde

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/1gde"
Personal tools