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.


1r0c

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1r0c" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r0c, resolution 2.37&Aring;" /> '''Products in the T St...)
Current revision (05:58, 23 August 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1r0c.jpg|left|200px]]<br /><applet load="1r0c" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1r0c, resolution 2.37&Aring;" />
 
-
'''Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme'''<br />
 
-
==Overview==
+
==Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme==
-
The structure of aspartate transcarbamylase of Escherichia coli ligated to, products (phosphate and N-carbamyl-l-aspartate) has been determined at, 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might, indicate a product release mode, rather than close analogues to the, transition state like those found in our earlier studies of other ligands, (N-phosphonacetyl-L-aspartate, carbamyl phosphate plus malonate, phosphonoacetamide plus malonate, or citrate plus phosphate). Ordered, product release, first carbamylaspartate (CLA) and then phosphate, might, be facilitated by a 4 A movement of phosphate from the substrate-analogue, position to the product (phosphate) binding position, and by a somewhat, similar release movement of the other product (CLA) relative to its, analogue (citrate). This movement is consistent with earlier studies of, binding of either pyrophosphate or phosphate alone [Honzatko, R. B., and, Lipscomb, W. N. (1982) J. Mol. Biol. 160, 265-286].
+
<StructureSection load='1r0c' size='340' side='right'caption='[[1r0c]], [[Resolution|resolution]] 2.37&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1r0c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R0C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R0C FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.37&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCD:N-CARBAMOYL-L-ASPARTATE'>NCD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1r0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r0c OCA], [https://pdbe.org/1r0c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r0c RCSB], [https://www.ebi.ac.uk/pdbsum/1r0c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r0c ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PYRB_ECOLI PYRB_ECOLI]
 +
== 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/r0/1r0c_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=1r0c ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The structure of aspartate transcarbamylase of Escherichia coli ligated to products (phosphate and N-carbamyl-l-aspartate) has been determined at 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might indicate a product release mode, rather than close analogues to the transition state like those found in our earlier studies of other ligands (N-phosphonacetyl-L-aspartate, carbamyl phosphate plus malonate, phosphonoacetamide plus malonate, or citrate plus phosphate). Ordered product release, first carbamylaspartate (CLA) and then phosphate, might be facilitated by a 4 A movement of phosphate from the substrate-analogue position to the product (phosphate) binding position, and by a somewhat similar release movement of the other product (CLA) relative to its analogue (citrate). This movement is consistent with earlier studies of binding of either pyrophosphate or phosphate alone [Honzatko, R. B., and Lipscomb, W. N. (1982) J. Mol. Biol. 160, 265-286].
-
==About this Structure==
+
Products in the T-state of aspartate transcarbamylase: crystal structure of the phosphate and N-carbamyl-L-aspartate ligated enzyme.,Huang J, Lipscomb WN Biochemistry. 2004 Jun 1;43(21):6422-6. PMID:15157076<ref>PMID:15157076</ref>
-
1R0C is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN, PO4 and NCD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase Aspartate carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.2 2.1.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R0C OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Products in the T-state of aspartate transcarbamylase: crystal structure of the phosphate and N-carbamyl-L-aspartate ligated enzyme., Huang J, Lipscomb WN, Biochemistry. 2004 Jun 1;43(21):6422-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15157076 15157076]
+
</div>
-
[[Category: Aspartate carbamoyltransferase]]
+
<div class="pdbe-citations 1r0c" style="background-color:#fffaf0;"></div>
-
[[Category: Escherichia coli]]
+
-
[[Category: Protein complex]]
+
-
[[Category: Huang, J.]]
+
-
[[Category: Lipscomb, W.N.]]
+
-
[[Category: NCD]]
+
-
[[Category: PO4]]
+
-
[[Category: ZN]]
+
-
[[Category: aspartate carbamoyltransferase]]
+
-
[[Category: aspartate transcarbamylase]]
+
-
[[Category: atcase-products complex]]
+
-
[[Category: n-carbamyl-l-aspartate(cla)]]
+
-
[[Category: phosphate]]
+
-
[[Category: products]]
+
-
[[Category: t state]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:09:32 2007''
+
==See Also==
 +
*[[Aspartate carbamoyltransferase 3D structures|Aspartate carbamoyltransferase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Escherichia coli]]
 +
[[Category: Large Structures]]
 +
[[Category: Huang J]]
 +
[[Category: Lipscomb WN]]

Current revision

Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme

PDB ID 1r0c

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/1r0c"
Personal tools