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.


3di1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:09, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3di1.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of the Staphylococcus aureus Dihydrodipicolinate synthase-pyruvate complex==
-
The line below this paragraph, containing "STRUCTURE_3di1", creates the "Structure Box" on the page.
+
<StructureSection load='3di1' size='340' side='right'caption='[[3di1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3di1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DI1 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
-
{{STRUCTURE_3di1| PDB=3di1 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3di1 OCA], [https://pdbe.org/3di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3di1 RCSB], [https://www.ebi.ac.uk/pdbsum/3di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3di1 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DAPA_STAAC DAPA_STAAC] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:18671976</ref>
 +
== 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/di/3di1_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=3di1 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.
-
===Crystal structure of the Staphylococcus aureus Dihydrodipicolinate synthase-pyruvate complex===
+
Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase.,Girish TS, Sharma E, Gopal B FEBS Lett. 2008 Aug 20;582(19):2923-30. Epub 2008 Jul 29. PMID:18671976<ref>PMID:18671976</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3di1" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18671976}}, adds the Publication Abstract to the page
+
*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18671976 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18671976}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3DI1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_col Staphylococcus aureus subsp. aureus col]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DI1 OCA].
+
[[Category: Staphylococcus aureus subsp. aureus COL]]
-
 
+
[[Category: Tavarekere GS]]
-
==Reference==
+
-
Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase., Girish TS, Sharma E, Gopal B, FEBS Lett. 2008 Aug 20;582(19):2923-30. Epub 2008 Jul 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18671976 18671976]
+
-
[[Category: Dihydrodipicolinate synthase]]
+
-
[[Category: Single protein]]
+
-
[[Category: Staphylococcus aureus subsp. aureus col]]
+
-
[[Category: Tavarekere, G S.]]
+
-
[[Category: Amino-acid biosynthesis]]
+
-
[[Category: Cytoplasm]]
+
-
[[Category: Diaminopimelate biosynthesis]]
+
-
[[Category: Dihydrodipicolinate synthase]]
+
-
[[Category: Feedback inhibition]]
+
-
[[Category: Lyase]]
+
-
[[Category: Lysine biosynthesis]]
+
-
[[Category: Ping-pong mechanism]]
+
-
[[Category: Schiff base]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 13 14:09:50 2008''
+

Current revision

Crystal structure of the Staphylococcus aureus Dihydrodipicolinate synthase-pyruvate complex

PDB ID 3di1

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/3di1"
Personal tools