2plq

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the amidase from geobacillus pallidus RAPc8

Structural highlights

2plq is a 1 chain structure with sequence from Aeribacillus pallidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMIE_BACSP Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia.^[1] Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates (By similarity).^[2]

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

The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.

The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.,Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891^[3]

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

References

↑ Kim S, Oriel P. Cloning and expression of the nitrile hydratase and amidase genes from Bacillus sp. BR449 into Escherichia coli. Enzyme Microb Technol. 2000 Oct 1;27(7):492-501. PMID:10978771
↑ Kim S, Oriel P. Cloning and expression of the nitrile hydratase and amidase genes from Bacillus sp. BR449 into Escherichia coli. Enzyme Microb Technol. 2000 Oct 1;27(7):492-501. PMID:10978771
↑ Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT. The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891 doi:10.1107/S1744309106043855

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/2plq"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2plq.png|left|200px]]
-<!--
+==Crystal structure of the amidase from geobacillus pallidus RAPc8==
-The line below this paragraph, containing "STRUCTURE_2plq", creates the "Structure Box" on the page.
+<StructureSection load='2plq' size='340' side='right'caption='[[2plq]], [[Resolution|resolution]] 1.90&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'>[[2plq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeribacillus_pallidus Aeribacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLQ 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]] 1.9&#8491;</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=2plq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plq OCA], [https://pdbe.org/2plq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plq RCSB], [https://www.ebi.ac.uk/pdbsum/2plq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plq ProSAT]</span></td></tr>
-{{STRUCTURE_2plq|  PDB=2plq  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMIE_BACSP AMIE_BACSP] Catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia.<ref>PMID:10978771</ref>   Also exhibits in vitro acyl transferase activity, transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates (By similarity).<ref>PMID:10978771</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/pl/2plq_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=2plq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.
-===Crystal structure of the amidase from geobacillus pallidus RAPc8===
+The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.,Agarkar VB, Kimani SW, Cowan DA, Sayed MF, Sewell BT Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1174-8. Epub 2006 Nov 4. PMID:17142891<ref>PMID:17142891</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17142891}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2plq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17142891 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17142891}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Aeribacillus pallidus]]
-PLQ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_pallidus Geobacillus pallidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLQ OCA].
+[[Category: Large Structures]]
+[[Category: Agarkar VB]]
-==Reference==
+[[Category: Cowan DA]]
-<ref group="xtra">PMID:17142891</ref><references group="xtra"/>
+[[Category: Kimani SW]]
-[[Category: Amidase]]
+[[Category: Sayed MF]]
-[[Category: Geobacillus pallidus]]
+[[Category: Sewell BT]]
-[[Category: Agarkar, V B.]]
-[[Category: Cowan, D A.]]
-[[Category: Kimani, S W.]]
-[[Category: Sayed, M F.]]
-[[Category: Sewell, B T.]]
-[[Category: Alpha-beta-beta-alpha]]
-[[Category: Nitrilase fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:51:43 2009''

2plq

From Proteopedia

Current revision

Crystal structure of the amidase from geobacillus pallidus RAPc8

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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