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2a81

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carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine

Structural highlights

2a81 is a 3 chain structure with sequence from Pectobacterium carotovorum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.15Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CARB_PECCC Catalyzes the formation of (2S,5S)-carboxymethylproline (t-CMP) from malonyl-CoA and (S)-1-pyrroline-5-carboxylate, the first step in the biosynthesis of (5R)-carbapen-2-em-3-carboxylate, a beta-lactam antibiotic of the carbapenem class (PubMed:15595850, PubMed:14625287). Also catalyzes the independent decarboxylation of malonyl-CoA and methylmalonyl-CoA and the hydrolysis of CoA esters such as acetyl-CoA and propionyl-CoA (PubMed:15595850). Catalyzes the reaction with a C2 epimeric mixture of methylmalonyl-CoA to give a 55:45 mixture of (6R)- and (6S)-epimers of 6-methyl-t-CMP, under standard incubation conditions (PubMed:21505494).^[1] ^[2] ^[3] ^[4] ^[5]

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 first step in the biosynthesis of the medicinally important carbapenem family of beta-lactam antibiotics is catalyzed by carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily. CarB catalyzes formation of (2S,5S)-carboxymethylproline [(2S,5S)-t-CMP] from malonyl-CoA and l-glutamate semialdehyde. In addition to using a cosubstrate, CarB catalyzes C-C and C-N bond formation processes as well as an acyl-coenzyme A hydrolysis reaction. We describe the crystal structure of CarB in the presence and absence of acetyl-CoA at 2.24 A and 3.15 A resolution, respectively. The structures reveal that CarB contains a conserved oxy-anion hole probably required for decarboxylation of malonyl-CoA and stabilization of the resultant enolate. Comparison of the structures reveals that conformational changes (involving His(229)) in the cavity predicted to bind l-glutamate semialdehyde occur on (co)substrate binding. Mechanisms for the formation of the carboxymethylproline ring are discussed in the light of the structures and the accompanying studies using isotopically labeled substrates; cyclization via 1,4-addition is consistent with the observed labeling results (providing that hydrogen exchange at the C-6 position of carboxymethylproline does not occur). The side chain of Glu(131) appears to be positioned to be involved in hydrolysis of the carboxymethylproline-CoA ester intermediate. Labeling experiments ruled out the possibility that hydrolysis proceeds via an anhydride in which water attacks a carbonyl derived from Glu(131), as proposed for 3-hydroxyisobutyryl-CoA hydrolase. The structural work will aid in mutagenesis studies directed at altering the selectivity of CarB to provide intermediates for the production of clinically useful carbapenems.

Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis.,Sleeman MC, Sorensen JL, Batchelar ET, McDonough MA, Schofield CJ J Biol Chem. 2005 Oct 14;280(41):34956-65. Epub 2005 Aug 11. PMID:16096274^[6]

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

References

↑ Sleeman MC, Schofield CJ. Carboxymethylproline synthase (CarB), an unusual carbon-carbon bond-forming enzyme of the crotonase superfamily involved in carbapenem biosynthesis. J Biol Chem. 2004 Feb 20;279(8):6730-6. Epub 2003 Nov 18. PMID:14625287 doi:http://dx.doi.org/10.1074/jbc.M311824200
↑ Gerratana B, Arnett SO, Stapon A, Townsend CA. Carboxymethylproline synthase from Pectobacterium carotorova: a multifaceted member of the crotonase superfamily. Biochemistry. 2004 Dec 21;43(50):15936-45. PMID:15595850 doi:http://dx.doi.org/10.1021/bi0483662
↑ Sorensen JL, Sleeman MC, Schofield CJ. Synthesis of deuterium labelled L- and D-glutamate semialdehydes and their evaluation as substrates for carboxymethylproline synthase (CarB)--implications for carbapenem biosynthesis. Chem Commun (Camb). 2005 Mar 7;(9):1155-7. Epub 2005 Jan 13. PMID:15726176 doi:http://dx.doi.org/10.1039/b416423g
↑ Batchelar ET, Hamed RB, Ducho C, Claridge TD, Edelmann MJ, Kessler B, Schofield CJ. Thioester hydrolysis and C-C bond formation by carboxymethylproline synthase from the crotonase superfamily. Angew Chem Int Ed Engl. 2008;47(48):9322-5. doi: 10.1002/anie.200803906. PMID:18972478 doi:http://dx.doi.org/10.1002/anie.200803906
↑ Hamed RB, Gomez-Castellanos JR, Thalhammer A, Harding D, Ducho C, Claridge TD, Schofield CJ. Stereoselective C-C bond formation catalysed by engineered carboxymethylproline synthases. Nat Chem. 2011 May;3(5):365-71. doi: 10.1038/nchem.1011. Epub 2011 Apr 3. PMID:21505494 doi:http://dx.doi.org/10.1038/nchem.1011
↑ Sleeman MC, Sorensen JL, Batchelar ET, McDonough MA, Schofield CJ. Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis. J Biol Chem. 2005 Oct 14;280(41):34956-65. Epub 2005 Aug 11. PMID:16096274 doi:10.1074/jbc.M507196200

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/2a81"

@@ Line 1: / Line 1: @@
 ==carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine==
-<StructureSection load='2a81' size='340' side='right' caption='[[2a81]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+<StructureSection load='2a81' size='340' side='right'caption='[[2a81]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2a81]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pectobacterium_carotovorum Pectobacterium carotovorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A81 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2a81]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pectobacterium_carotovorum Pectobacterium carotovorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A81 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=BCN:BICINE'>BCN</scene><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]] 3.15&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2a7k|2a7k]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=BCN:BICINE'>BCN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CarB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=554 Pectobacterium carotovorum])</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=2a81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a81 OCA], [https://pdbe.org/2a81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a81 RCSB], [https://www.ebi.ac.uk/pdbsum/2a81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a81 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a81 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a81 RCSB], [http://www.ebi.ac.uk/pdbsum/2a81 PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/CARB_PECCC CARB_PECCC] Catalyzes the formation of (2S,5S)-carboxymethylproline (t-CMP) from malonyl-CoA and (S)-1-pyrroline-5-carboxylate, the first step in the biosynthesis of (5R)-carbapen-2-em-3-carboxylate, a beta-lactam antibiotic of the carbapenem class (PubMed:15595850, PubMed:14625287). Also catalyzes the independent decarboxylation of malonyl-CoA and methylmalonyl-CoA and the hydrolysis of CoA esters such as acetyl-CoA and propionyl-CoA (PubMed:15595850). Catalyzes the reaction with a C2 epimeric mixture of methylmalonyl-CoA to give a 55:45 mixture of (6R)- and (6S)-epimers of 6-methyl-t-CMP, under standard incubation conditions (PubMed:21505494).<ref>PMID:14625287</ref> <ref>PMID:15595850</ref> <ref>PMID:15726176</ref> <ref>PMID:18972478</ref> <ref>PMID:21505494</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/a8/2a81_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a8/2a81_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=2a81 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2a81" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pectobacterium carotovorum]]
-[[Category: Batchelar, E T.]]
+[[Category: Batchelar ET]]
-[[Category: McDonough, M A.]]
+[[Category: McDonough MA]]
-[[Category: Schofield, C J.]]
+[[Category: Schofield CJ]]
-[[Category: Sleeman, M C.]]
+[[Category: Sleeman MC]]
-[[Category: Sorensen, J L.]]
+[[Category: Sorensen JL]]
-[[Category: Acetyl coenzyme some]]
-[[Category: Antibiotic]]
-[[Category: Beta-lactam]]
-[[Category: Bicine]]
-[[Category: Biosynthetic protein]]
-[[Category: Carbapenam]]
-[[Category: Carbapenem]]
-[[Category: Crotonase]]

2a81

From Proteopedia

Current revision

carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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