1b7b: Difference between revisions
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< | ==Carbamate kinase from Enterococcus faecalis== | ||
<StructureSection load='1b7b' size='340' side='right'caption='[[1b7b]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1b7b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B7B 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]] 2.8Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b7b OCA], [https://pdbe.org/1b7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b7b RCSB], [https://www.ebi.ac.uk/pdbsum/1b7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b7b ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ARCC1_ENTFC ARCC1_ENTFC] 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/b7/1b7b_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=1b7b ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The enzymes carbamoyl phosphate synthetase (CPS) and carbamate kinase (CK) make carbamoyl phosphate in the same way: by ATP-phosphorylation of carbamate. The carbamate used by CK is made chemically, whereas CPS itself synthesizes its own carbamate in a process involving the phosphorylation of bicarbonate. Bicarbonate and carbamate are analogs and the phosphorylations are carried out by homologous 40 kDa regions of the 120 kDa CPS polypeptide. CK can also phosphorylate bicarbonate and is a homodimer of a 33 kDa subunit that was believed to resemble the 40 kDa regions of CPS. Such belief is disproven now by the CK structure reported here. The structure does not conform to the biotin carboxylase fold found in the 40 kDa regions of CPS, and presents a new type of fold possibly shared by homologous acylphosphate-making enzymes. A molecular 16-stranded open beta-sheet surrounded by alpha-helices is the hallmark of the CK dimer. Each subunit also contains two smaller sheets and a large crevice found at the location expected for the active center. Intersubunit interactions are very large and involve a central hydrophobic patch and more hydrophilic peripheral contacts. The crevice holds a sulfate that may occupy the site of an ATP phosphate, and is lined by conserved residues. Site-directed mutations tested at two of these residues inactivate the enzyme. These findings support active site location in the crevice. The orientation of the crevices in the dimer precludes their physical cooperation in the catalytic process. Such cooperation is not needed in the CK reaction but is a requirement of the mechanism of CPSs. | |||
Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.,Marina A, Alzari PM, Bravo J, Uriarte M, Barcelona B, Fita I, Rubio V Protein Sci. 1999 Apr;8(4):934-40. PMID:10211841<ref>PMID:10211841</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1b7b" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Enterococcus faecium]] | [[Category: Enterococcus faecium]] | ||
[[Category: Alzari | [[Category: Large Structures]] | ||
[[Category: Barcelona | [[Category: Alzari PM]] | ||
[[Category: Bravo | [[Category: Barcelona B]] | ||
[[Category: Fita | [[Category: Bravo J]] | ||
[[Category: Marina | [[Category: Fita I]] | ||
[[Category: Rubio | [[Category: Marina A]] | ||
[[Category: Uriarte | [[Category: Rubio V]] | ||
[[Category: Uriarte M]] | |||
Latest revision as of 02:20, 28 December 2023
Carbamate kinase from Enterococcus faecalisCarbamate kinase from Enterococcus faecalis
Structural highlights
FunctionARCC1_ENTFC 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 PubMedThe enzymes carbamoyl phosphate synthetase (CPS) and carbamate kinase (CK) make carbamoyl phosphate in the same way: by ATP-phosphorylation of carbamate. The carbamate used by CK is made chemically, whereas CPS itself synthesizes its own carbamate in a process involving the phosphorylation of bicarbonate. Bicarbonate and carbamate are analogs and the phosphorylations are carried out by homologous 40 kDa regions of the 120 kDa CPS polypeptide. CK can also phosphorylate bicarbonate and is a homodimer of a 33 kDa subunit that was believed to resemble the 40 kDa regions of CPS. Such belief is disproven now by the CK structure reported here. The structure does not conform to the biotin carboxylase fold found in the 40 kDa regions of CPS, and presents a new type of fold possibly shared by homologous acylphosphate-making enzymes. A molecular 16-stranded open beta-sheet surrounded by alpha-helices is the hallmark of the CK dimer. Each subunit also contains two smaller sheets and a large crevice found at the location expected for the active center. Intersubunit interactions are very large and involve a central hydrophobic patch and more hydrophilic peripheral contacts. The crevice holds a sulfate that may occupy the site of an ATP phosphate, and is lined by conserved residues. Site-directed mutations tested at two of these residues inactivate the enzyme. These findings support active site location in the crevice. The orientation of the crevices in the dimer precludes their physical cooperation in the catalytic process. Such cooperation is not needed in the CK reaction but is a requirement of the mechanism of CPSs. Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.,Marina A, Alzari PM, Bravo J, Uriarte M, Barcelona B, Fita I, Rubio V Protein Sci. 1999 Apr;8(4):934-40. PMID:10211841[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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