3i7r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:40, 6 September 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3i7r.png|left|200px]]
 
-
<!--
+
==Dihydrodipicolinate synthase - K161R==
-
The line below this paragraph, containing "STRUCTURE_3i7r", creates the "Structure Box" on the page.
+
<StructureSection load='3i7r' size='340' side='right'caption='[[3i7r]], [[Resolution|resolution]] 2.10&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'>[[3i7r]] 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=3I7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7R 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]] 2.1&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
{{STRUCTURE_3i7r| PDB=3i7r | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3i7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7r OCA], [https://pdbe.org/3i7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7r RCSB], [https://www.ebi.ac.uk/pdbsum/3i7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7r ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</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/i7/3i7r_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=3i7r ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a validated antibiotic target, catalyses the first committed step in the lysine biosynthetic pathway: the condensation reaction between (S)-aspartate beta-semialdehyde [(S)-ASA] and pyruvate via the formation of a Schiff base intermediate between pyruvate and the absolutely conserved active-site lysine. Escherichia coli DHDPS mutants K161A and K161R of the active-site lysine were characterised for the first time. Unexpectedly, the mutant enzymes were still catalytically active, albeit with a significant decrease in activity. The k(cat) values for DHDPS-K161A and DHDPS-K161R were 0.06 +/- 0.02 s(-1) and 0.16 +/- 0.06 s(-1) respectively, compared to 45 +/- 3 s(-1) for the wild-type enzyme. Remarkably, the K(M) values for pyruvate increased by only 3-fold for DHDPS-K161A and DHDPS-K161R (0.45 +/- 0.04 mM and 0.57 +/- 0.06 mM, compared to 0.15 +/- 0.01 mM for the wild-type DHDPS), while the K(M) values for (S)-ASA remained the same for DHDPS-K161R (0.12 +/- 0.01 mM) and increased by only 2-fold for DHDPS-K161A (0.23 +/- 0.02 mM) and the K(i) for lysine was unchanged. The X-ray crystal structures of DHDPS-K161A and DHDPS-K161R were solved at resolutions of 2.0 and 2.1 A respectively and showed no changes in their secondary or tertiary structures when compared to the wild-type structure. The crystal structure of DHDPS-K161A with pyruvate bound at the active site was solved at a resolution of 2.3 A and revealed a defined binding pocket for pyruvate that is thus not dependent upon lysine 161. Taken together with ITC and NMR data, it is concluded that although lysine 161 is important in the wild-type DHDPS-catalysed reaction, it is not absolutely essential for catalysis.
-
===Dihydrodipicolinate synthase - K161R===
+
How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase?,Soares da Costa TP, Muscroft-Taylor AC, Dobson RC, Devenish SR, Jameson GB, Gerrard JA Biochimie. 2010 Jul;92(7):837-45. Epub 2010 Mar 29. PMID:20353808<ref>PMID:20353808</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3i7r" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20353808}}, adds the Publication Abstract to the page
+
*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20353808 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20353808}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Escherichia coli K-12]]
-
3I7R is a 2 chains structure with sequences from [http://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=3I7R OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Dobson RCJ]]
-
==Reference==
+
[[Category: Gerrard JA]]
-
<ref group="xtra">PMID:20353808</ref><references group="xtra"/>
+
[[Category: Jameson GB]]
-
[[Category: Dihydrodipicolinate synthase]]
+
[[Category: Soares da Costa TP]]
-
[[Category: Escherichia coli k-12]]
+
-
[[Category: Costa, T P.Soares da.]]
+
-
[[Category: Dobson, R C.J.]]
+
-
[[Category: Gerrard, J A.]]
+
-
[[Category: Jameson, G B.]]
+
-
[[Category: Amino-acid biosynthesis]]
+
-
[[Category: Diaminopimelate biosynthesis]]
+
-
[[Category: Dihydrodipicolinate synthase]]
+
-
[[Category: Lyase]]
+
-
[[Category: Lysine biosynthesis]]
+
-
[[Category: Schiff base]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 08:18:40 2010''
+

Current revision

Dihydrodipicolinate synthase - K161R

PDB ID 3i7r

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/3i7r"
Personal tools