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.


1fy6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:20, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1fy6.jpg|left|200px]]
 
-
{{Structure
+
==AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P==
-
|PDB= 1fy6 |SIZE=350|CAPTION= <scene name='initialview01'>1fy6</scene>, resolution 1.89&Aring;
+
<StructureSection load='1fy6' size='340' side='right'caption='[[1fy6]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> and <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>
+
<table><tr><td colspan='2'>[[1fy6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FY6 FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1fy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fy6 OCA], [https://pdbe.org/1fy6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fy6 RCSB], [https://www.ebi.ac.uk/pdbsum/1fy6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fy6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
 +
== 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/fy/1fy6_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=1fy6 ConSurf].
 +
<div style="clear:both"></div>
-
'''AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P'''
+
==See Also==
-
 
+
*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
3-Deoxy-D-manno-octulosonate-8-phosphate synthase (KDO8PS) from the hyperthermophilic bacterium Aquifex aeolicus differs from its Escherichia coli counterpart in the requirement of a divalent metal for activity (Duewel, H. S., and Woodard, R. W. (2000) J. Biol. Chem. 275, 22824-22831). Here we report the crystal structure of the A. aeolicus enzyme, which was determined by molecular replacement using E. coli KDO8PS as a model. The structures of the metal-free and Cd(2+) forms of the enzyme were determined in the uncomplexed state and in complex with various combinations of phosphoenolpyruvate (PEP), arabinose 5-phosphate (A5P), and erythrose 4-phosphate (E4P). Like the E. coli enzyme, A. aeolicus KDO8PS is a homotetramer containing four distinct active sites at the interface between subunits. The active site cavity is open in the substrate-free enzyme or when either A5P alone or PEP alone binds, and becomes isolated from the aqueous phase when both PEP and A5P (or E4P) bind together. In the presence of metal, the enzyme is asymmetric and appears to alternate catalysis between the active sites located on one face of the tetramer and those located on the other face. In the absence of metal, the asymmetry is lost. Details of the active site that may be important for catalysis are visible at the high resolution achieved in these structures. Most notably, the shape of the PEP-binding pocket forces PEP to assume a distorted geometry at C-2, which might anticipate the conversion from sp(2) to sp(3) hybridization occurring during intermediate formation and which may modulate PEP reactivity toward A5P. Two water molecules are located in van der Waals contact with the si and re sides of C-2(PEP), respectively. Abstraction of a proton from either of these water molecules by a protein group is expected to elicit a nucleophilic attack of the resulting hydroxide ion on the nearby C-2(PEP), thus triggering the beginning of the catalytic cycle.
+
-
 
+
-
==About this Structure==
+
-
1FY6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FY6 OCA].
+
-
 
+
-
==Reference==
+
-
Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism., Duewel HS, Radaev S, Wang J, Woodard RW, Gatti DL, J Biol Chem. 2001 Mar 16;276(11):8393-402. Epub 2000 Dec 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11115499 11115499]
+
-
[[Category: 3-deoxy-8-phosphooctulonate synthase]]
+
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Duewel, H S.]]
+
[[Category: Duewel HS]]
-
[[Category: Gatti, D L.]]
+
[[Category: Gatti DL]]
-
[[Category: Radaev, S.]]
+
[[Category: Radaev S]]
-
[[Category: Wang, J.]]
+
[[Category: Wang J]]
-
[[Category: Woodard, R W.]]
+
[[Category: Woodard RW]]
-
[[Category: A5P]]
+
-
[[Category: CD]]
+
-
[[Category: PO4]]
+
-
[[Category: a5p]]
+
-
[[Category: beta/alpha barrel]]
+
-
[[Category: kdo]]
+
-
[[Category: kdo8p]]
+
-
[[Category: kdo8p]]
+
-
[[Category: pep]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:15:36 2008''
+

Current revision

AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P

PDB ID 1fy6

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/1fy6"
Personal tools