2a7k: Difference between revisions

Latest revision as of 09:11, 14 February 2024

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

Structural highlights

2a7k is a 9 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 2.24Å
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.

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:https://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:https://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:https://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:https://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:https://dx.doi.org/10.1038/nchem.1011

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1074/jbc.M311824200

[2] 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:https://dx.doi.org/10.1021/bi0483662

[3] 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:https://dx.doi.org/10.1039/b416423g

[4] 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:https://dx.doi.org/10.1002/anie.200803906

[5] 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:https://dx.doi.org/10.1038/nchem.1011

[1]

[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='2a7k' size='340' side='right'caption='[[2a7k]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2a7k]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_carotovorus"_jones_1901 "bacillus carotovorus" jones 1901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A7K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2a7k]] is a 9 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=2A7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A7K FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CarB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=554 "Bacillus carotovorus" Jones 1901])</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]] 2.24&#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=2a7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a7k OCA], [https://pdbe.org/2a7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a7k RCSB], [https://www.ebi.ac.uk/pdbsum/2a7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a7k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/Q9XB60_PECCA Q9XB60_PECCA]] 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>
+[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]]
@@ Line 19: / Line 19: @@
 </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=2a7k ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== 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<ref>PMID:16096274</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2a7k" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus carotovorus jones 1901]]
 [[Category: Large Structures]]
-[[Category: Batchelar, E T]]
+[[Category: Pectobacterium carotovorum]]
-[[Category: McDonough, M A]]
+[[Category: Batchelar ET]]
-[[Category: Schofield, C J]]
+[[Category: McDonough MA]]
-[[Category: Sleeman, M C]]
+[[Category: Schofield CJ]]
-[[Category: Sorensen, J L]]
+[[Category: Sleeman MC]]
-[[Category: Antibiotic]]
+[[Category: Sorensen JL]]
-[[Category: Beta-lactam]]
-[[Category: Biosynthetic protein]]
-[[Category: Carbapenam]]
-[[Category: Carbapenem]]
-[[Category: Crotonase]]

2a7k: Difference between revisions

Latest revision as of 09:11, 14 February 2024

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

Structural highlights

Function

Evolutionary Conservation

References

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