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2we4

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Current revision

Carbamate kinase from Enterococcus faecalis bound to a sulfate ion and two water molecules, which mimic the substrate carbamyl phosphate

Structural highlights

2we4 is a 4 chain structure with sequence from Enterococcus faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.02Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARCC1_ENTFA Catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP. Can also catalyze, although with low efficiency, the phosphorylation of bicarbonate, leading to the formation of carboxyphosphate, an unstable intermediate found in the reactions catalyzed by carbamoyl-phosphate synthase and biotin carboxylase. Can also use acetate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Carbamate kinase (CK) makes ATP from ADP and carbamoyl phosphate (CP) in the final step of the microbial fermentative catabolism of arginine, agmatine, and oxalurate/allantoin. Two previously reported CK structures failed to clarify CP binding and catalysis and to reveal the significance of the protruding subdomain (PSD) that hangs over the CK active center as an exclusive and characteristic CK feature. We clarify now these three questions by determining two crystal structures of Enterococcus faecalis CK (one at 1.5 A resolution and containing bound MgADP, and the other at 2.1 A resolution and having in the active center one sulfate and two fixed water molecules that mimic one bound CP molecule) and by mutating active-center residues, determining the consequences of these mutations on enzyme functionality. Superimposition of the present crystal structures reconstructs the filled active center in the ternary complex, immediately suggesting in-line associative phosphoryl group transfer and a mechanism for enzyme catalysis involving N51, K209, K271, D210, and the PSD residue K128. The large respective increases and decreases in K(m)(CP) and k(cat) triggered by the mutations N51A, K128A, K209A, and D210N corroborate the ternary complex active-site architecture and the catalytic mechanism proposed. The extreme negative effects of K128A demonstrate a key role of the PSD in substrate binding and catalysis. The crystal structures reveal large rigid-body movements of the PSD towards the enzyme body that place K128 next to CP and bury the CP site. A mechanism that connects CP site occupation with the PSD approach, involving V206-I207 in the CP site and P162-S163 in the PSD stem, is identified. The effects of the V206A and V206L mutations support this mechanism. It is concluded that the PSD movement allows CK to select against the abundant CP/carbamate analogues acetylphosphate/acetate and bicarbonate, rendering CK highly selective for CP/carbamate.

Substrate binding and catalysis in carbamate kinase ascertained by crystallographic and site-directed mutagenesis studies: movements and significance of a unique globular subdomain of this key enzyme for fermentative ATP production in bacteria.,Ramon-Maiques S, Marina A, Guinot A, Gil-Ortiz F, Uriarte M, Fita I, Rubio V J Mol Biol. 2010 Apr 16;397(5):1261-75. Epub 2010 Feb 25. PMID:20188742^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ramon-Maiques S, Marina A, Guinot A, Gil-Ortiz F, Uriarte M, Fita I, Rubio V. Substrate binding and catalysis in carbamate kinase ascertained by crystallographic and site-directed mutagenesis studies: movements and significance of a unique globular subdomain of this key enzyme for fermentative ATP production in bacteria. J Mol Biol. 2010 Apr 16;397(5):1261-75. Epub 2010 Feb 25. PMID:20188742 doi:10.1016/j.jmb.2010.02.038

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2we4"

@@ Line 1: / Line 1: @@
 ==Carbamate kinase from Enterococcus faecalis bound to a sulfate ion and two water molecules, which mimic the substrate carbamyl phosphate==
-<StructureSection load='2we4' size='340' side='right' caption='[[2we4]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+<StructureSection load='2we4' size='340' side='right'caption='[[2we4]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2we4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WE4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WE4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2we4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WE4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.02&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2we5|2we5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamate_kinase Carbamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.2 2.7.2.2] </span></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=2we4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2we4 OCA], [https://pdbe.org/2we4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2we4 RCSB], [https://www.ebi.ac.uk/pdbsum/2we4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2we4 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2we4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2we4 OCA], [http://pdbe.org/2we4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2we4 RCSB], [http://www.ebi.ac.uk/pdbsum/2we4 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ARCC1_ENTFA ARCC1_ENTFA]] Catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP. Can also catalyze, although with low efficiency, the phosphorylation of bicarbonate, leading to the formation of carboxyphosphate, an unstable intermediate found in the reactions catalyzed by carbamoyl-phosphate synthase and biotin carboxylase. Can also use acetate.
+[https://www.uniprot.org/uniprot/ARCC1_ENTFA ARCC1_ENTFA] Catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP. Can also catalyze, although with low efficiency, the phosphorylation of bicarbonate, leading to the formation of carboxyphosphate, an unstable intermediate found in the reactions catalyzed by carbamoyl-phosphate synthase and biotin carboxylase. Can also use acetate.
 == 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/we/2we4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/we/2we4_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2we4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
+[[Category: Enterococcus faecalis]]
-[[Category: Carbamate kinase]]
+[[Category: Large Structures]]
-[[Category: Gil-Ortiz, F]]
+[[Category: Gil-Ortiz F]]
-[[Category: Marina, A]]
+[[Category: Marina A]]
-[[Category: Ramon-Maiques, S]]
+[[Category: Ramon-Maiques S]]
-[[Category: Rubio, V]]
+[[Category: Rubio V]]
-[[Category: Arginine catabolism]]
-[[Category: Arginine metabolism]]
-[[Category: Atp synthesy]]
-[[Category: Kinase]]
-[[Category: Open alpha/beta sheet]]
-[[Category: Phosphotransferase]]
-[[Category: Transferase]]

2we4

From Proteopedia

Current revision

Carbamate kinase from Enterococcus faecalis bound to a sulfate ion and two water molecules, which mimic the substrate carbamyl phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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