6N96 | pdb_00006n96

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA

PDB DOI: https://doi.org/10.2210/pdb6N96/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-11-30 Released: 2019-04-10
Deposition Author(s): Stunkard, L.M., Dixon, A.D., Huth, T.J., Lohman, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.184 (Depositor), 0.192 (DCC)
R-Value Work:
0.151 (Depositor), 0.163 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.

Stunkard, L.M., Dixon, A.D., Huth, T.J., Lohman, J.R.

(2019) J Am Chem Soc 141: 5121-5124

PubMed: 30869886 Search on PubMed
DOI: https://doi.org/10.1021/jacs.9b00650
Primary Citation Related Structures:
6N92, 6N93, 6N94, 6N95, 6N96, 6N97

PubMed Abstract:
Malonyl-thioesters are reactive centers of malonyl-CoA and malonyl- S-acyl carrier protein, essential to fatty acid, polyketide and various specialized metabolite biosynthesis. Enzymes that create or use malonyl-thioesters spontaneously hydrolyze or decarboxylate reactants on the crystallographic time frame preventing determination of structure-function relationships. To address this problem, we have synthesized a panel of methylmalonyl-CoA analogs with the carboxylate represented by a sulfonate or nitro and the thioester retained or represented by an ester or amide. Structures of Escherichia coli methylmalonyl-CoA decarboxylase in complex with our analogs affords insight into substrate binding and the catalytic mechanism. Counterintuitively, the negatively charged sulfonate and nitronate functional groups of our analogs bind in an active site hydrophobic pocket. Upon decarboxylation the enolate intermediate is protonated by a histidine preventing CO ₂-enolate recombination, yielding propionyl-CoA. Activity assays support a histidine catalytic acid and reveal the enzyme displays significant hydrolysis activity. Our structures also provide insight into this hydrolysis activity. Our analogs inhibit decarboxylation/hydrolysis activity with low micromolar K _i values. This study sets precedents for using malonyl-CoA analogs with carboxyate isosteres to study the complicated structure-function relationships of acyl-CoA carboxylases, trans-carboxytransferases, malonyltransferases and β-ketoacylsynthases.

Organizational Affiliation

Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States.

Macromolecule Content

Total Structure Weight: 187.64 kDa
Atom Count: 15,313
Modeled Residue Count: 1,560
Deposited Residue Count: 1,566
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA decarboxylase	A, B, C, D, E A, B, C, D, E, F	261	Escherichia coli K-12	Mutation(s): 1 Gene Names: scpB, mmcD, ygfG, b2919, JW2886 EC: 4.1.1
UniProt
Find proteins for P52045 (Escherichia coli (strain K12)) Explore P52045 Go to UniProtKB: P52045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52045
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO5 Query on SO5 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F]	H [auth A] J [auth B] L [auth C] O [auth D] R [auth E] H [auth A], J [auth B], L [auth C], O [auth D], R [auth E], T [auth F]	(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid C₂₄ H₄₀ N₇ O₂₁ P₃ S BEMUOEZGNHFKKE-AGCMQPJKSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F]
LCV Query on LCV Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth F]	G [auth A] I [auth B] K [auth C] M [auth C] N [auth D] G [auth A], I [auth B], K [auth C], M [auth C], N [auth D], Q [auth E], S [auth F], U [auth F]	(2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid C₂₄ H₄₀ N₇ O₂₁ P₃ S BEMUOEZGNHFKKE-IBNUZSNCSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth F]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]