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Escherichia coli K-12 substr. MG1655 Enzyme: murein DD-endopeptidase, penicillin-insensitive



Gene: mepA Accession Numbers: EG10580 (EcoCyc), b2328, ECK2322

Regulation Summary Diagram: ?

Subunit composition of murein DD-endopeptidase, penicillin-insensitive = [MepA]2

Summary:
MepA is a penicillin-insensitive DD endopeptidase which hydrolyses both DD (meso-A2pm-D-Ala) and LD (meso-A2pm-meso-A2pm) bonds within cell wall peptidoglycan peptide crosslinks.

The structure of MepA has been determined to resolutions of 1.4 and 2.4 Å [Marcyjaniak04]. MepA is a dimer that is localized in the periplasm by its amino-terminal signal peptide [Marcyjaniak04, Iida83, Keck90]. MepA is similar to proteins in the LAS metallopeptidase family. Mutations in putative zinc-coordinating residues histidine-113, aspartate-120 and histidine-211 inactivate MepA, as do metal chelators [Marcyjaniak04]. Mutation experiments reveal residue D120 is required for folding, while H113 and H211 are required for catalysis [Firczuk07]. Mutations of H206, H209, and H110 also reduce activity of the enzyme but are not required for folding [Firczuk07]. Residue W203 is important for substrate binding [Firczuk07]. MepA forms 3 intramolecular disulphide bonds catalyzed by DsbC [Hiniker04, Marcyjaniak04].

mepA mutants have reduced DD-endopeptidase activity, but grow normally [Iida83]. Purified MepA is able to hydrolyze D-alanyl-DAP and DAP-DAP amide bonds within peptidoglycan polymer [Tomioka78, Engel92]. Overproduction of MepA results in increased amounts of tri- and tetra-peptides released into the medium in a peptide-uptake mutant [Keck90]. Overproduction of MepA does not result in a reduced proportion of crosslinks in the peptidoglycan layer suggesting the enzyme acts in a progressive manner, possibly as part of a complex, rather than at random [Keck90]. MepA is able to digest thickened peptidoglycan septal rings that form due to the absence of AmiABC [Heidrich01].

The mepA gene is upregulated under basic, oxygen-limited conditions [Hayes06], and expression was lowest at neutral pH under aeration [Maurer05]. Expression of mepA was also repressed by acivicin treatment [Smulski01]. When cells were grown in rich medium, mepA was not expressed [Wei01].

Reviews: [Scheffers05, Vollmer04]

Citations: [Priyadarshini06, Huber05a, Korsak05, Bochtler04, Meisel03, Heidrich02, Kraft99, Denome99, Romeis94a, Engel92a, Burman83]

Locations: periplasmic space

Map Position: [2,443,582 <- 2,444,406] (52.67 centisomes)
Length: 825 bp / 274 aa

Molecular Weight of Polypeptide: 30.137 kD (from nucleotide sequence), 30.0 kD (experimental) [Keck79 ]

pI: 6.8 [Keck79]

Unification Links: ASAP:ABE-0007691 , CGSC:17650 , EchoBASE:EB0575 , EcoGene:EG10580 , EcoliWiki:b2328 , OU-Microarray:b2328 , PortEco:mepA , PR:PRO_000023207 , Pride:P0C0T5 , Protein Model Portal:P0C0T5 , RefSeq:NP_416831 , RegulonDB:EG10580 , SMR:P0C0T5 , String:511145.b2328 , UniProt:P0C0T5

Relationship Links: InterPro:IN-FAMILY:IPR005073 , InterPro:IN-FAMILY:IPR009045 , PDB:Structure:1tzp , PDB:Structure:1TZP , PDB:Structure:1u10 , PDB:Structure:1U10 , Pfam:IN-FAMILY:PF03411

In Paralogous Gene Group: 90 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000270 - peptidoglycan metabolic process Inferred from experiment Inferred by computational analysis [GOA06, Iida83, Keck90, Heidrich01, Engel92]
GO:0009252 - peptidoglycan biosynthetic process Inferred from experiment [Engel92]
GO:0042493 - response to drug Inferred from experiment [Smulski01]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004175 - endopeptidase activity Inferred from experiment [Iida83, Keck90]
GO:0008233 - peptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Keck90, Engel92]
GO:0004222 - metalloendopeptidase activity Inferred by computational analysis [GOA06]
GO:0004252 - serine-type endopeptidase activity Inferred by computational analysis [GOA01a]
GO:0008237 - metallopeptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [GOA01a, DiazMejia09, Iida83]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: cell processes protection drug resistance/sensitivity
cell structure murein
metabolism biosynthesis of macromolecules (cellular constituents) murein (peptidoglycan)

Essentiality data for mepA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 14-Jul-2008 by Johnson A , JCVI


Enzymatic reaction of: murein LD-endopeptidase (murein DD-endopeptidase, penicillin-insensitive)

EC Number: 3.4.-.-

peptidoglycan DAP-DAP crosslink[periplasmic space] + H2O[periplasmic space] <=> peptidoglycan tripeptide, glycan chain 1[periplasmic space] + peptidoglycan tetrapeptide, glycan chain 2[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: murein DD-endopeptidase

EC Number: 3.4.-.-

peptidoglycan D-alanyl-DAP crosslink[periplasmic space] + H2O[periplasmic space] <=> peptidoglycan tetrapeptide, glycan chain 2[periplasmic space] + peptidoglycan tetrapeptide, glycan chain 1[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

pH(opt): 6.0 [Keck79]


Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 19 MepA signal sequence
[Keck90]
 
Chain 20 -> 274  
[UniProt09]
UniProt: Penicillin-insensitive murein endopeptidase;
Disulfide-Bond-Site 265, 44  
[UniProt10]
Metal-Binding-Site 110  
[UniProt10]
UniProt: Zinc 1;
Mutagenesis-Variant 113  
[Marcyjaniak04, UniProt11]
Alternate sequence: H → A; UniProt: Strongly reduces enzyme activity.
Metal-Binding-Site 113  
[UniProt10]
UniProt: Zinc 1;
Mutagenesis-Variant 120  
[Marcyjaniak04, UniProt11]
Alternate sequence: D → A; UniProt: Strongly reduces enzyme activity.
Metal-Binding-Site 120  
[UniProt10]
UniProt: Zinc 1;
Metal-Binding-Site 147  
[UniProt10]
UniProt: Zinc 2;
Metal-Binding-Site 150  
[UniProt10]
UniProt: Zinc 2;
Disulfide-Bond-Site 235, 187  
[UniProt10]
Mutagenesis-Variant 209  
[Marcyjaniak04, UniProt11]
Alternate sequence: H → A; UniProt: Strongly reduces enzyme activity.
Mutagenesis-Variant 211  
[Marcyjaniak04, UniProt11]
Alternate sequence: H → A; UniProt: Strongly reduces enzyme activity.
Metal-Binding-Site 211  
[UniProt10]
UniProt: Zinc 1;
Disulfide-Bond-Site 223, 216  
[UniProt10]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2328 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10580; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bochtler04: Bochtler M, Odintsov SG, Marcyjaniak M, Sabala I (2004). "Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases." Protein Sci 13(4);854-61. PMID: 15044722

Burman83: Burman LG, Reichler J, Park JT (1983). "Evidence for multisite growth of Escherichia coli murein involving concomitant endopeptidase and transpeptidase activities." J Bacteriol 156(1);386-92. PMID: 6352683

Denome99: Denome SA, Elf PK, Henderson TA, Nelson DE, Young KD (1999). "Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis." J Bacteriol 181(13);3981-93. PMID: 10383966

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Engel92: Engel H, van Leeuwen A, Dijkstra A, Keck W (1992). "Enzymatic preparation of 1,6-anhydro-muropeptides by immobilized murein hydrolases from Escherichia coli fused to staphylococcal protein A." Appl Microbiol Biotechnol 37(6);772-83. PMID: 1369491

Engel92a: Engel H, Smink AJ, van Wijngaarden L, Keck W (1992). "Murein-metabolizing enzymes from Escherichia coli: existence of a second lytic transglycosylase." J Bacteriol 174(20);6394-403. PMID: 1356966

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Firczuk07: Firczuk M, Bochtler M (2007). "Mutational analysis of peptidoglycan amidase MepA." Biochemistry 46(1);120-8. PMID: 17198381

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hayes06: Hayes ET, Wilks JC, Sanfilippo P, Yohannes E, Tate DP, Jones BD, Radmacher MD, BonDurant SS, Slonczewski JL (2006). "Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12." BMC Microbiol 6;89. PMID: 17026754

Heidrich01: Heidrich C, Templin MF, Ursinus A, Merdanovic M, Berger J, Schwarz H, de Pedro MA, Holtje JV (2001). "Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli." Mol Microbiol 41(1);167-78. PMID: 11454209

Heidrich02: Heidrich C, Ursinus A, Berger J, Schwarz H, Holtje JV (2002). "Effects of multiple deletions of murein hydrolases on viability, septum cleavage, and sensitivity to large toxic molecules in Escherichia coli." J Bacteriol 184(22);6093-9. PMID: 12399477

Hiniker04: Hiniker A, Bardwell JC (2004). "In vivo substrate specificity of periplasmic disulfide oxidoreductases." J Biol Chem 279(13);12967-73. PMID: 14726535

Huber05a: Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J (2005). "Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation." J Bacteriol 187(9);2983-91. PMID: 15838024

Iida83: Iida K, Hirota Y, Schwarz U (1983). "Mutants of Escherichia coli defective in penicillin-insensitive murein DD-endopeptidase." Mol Gen Genet 189(2);215-21. PMID: 6343788

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Keck79: Keck W, Schwarz U (1979). "Escherichia coli murein-DD-endopeptidase insensitive to beta-lactam antibiotics." J Bacteriol 139(3);770-4. PMID: 383691

Keck90: Keck W, van Leeuwen AM, Huber M, Goodell EW (1990). "Cloning and characterization of mepA, the structural gene of the penicillin-insensitive murein endopeptidase from Escherichia coli." Mol Microbiol 4(2);209-19. PMID: 2187143

Korsak05: Korsak D, Liebscher S, Vollmer W (2005). "Susceptibility to antibiotics and beta-lactamase induction in murein hydrolase mutants of Escherichia coli." Antimicrob Agents Chemother 49(4);1404-9. PMID: 15793119

Kraft99: Kraft AR, Prabhu J, Ursinus A, Holtje JV (1999). "Interference with murein turnover has no effect on growth but reduces beta-lactamase induction in Escherichia coli." J Bacteriol 181(23);7192-8. PMID: 10572120

Marcyjaniak04: Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M (2004). "Peptidoglycan amidase MepA is a LAS metallopeptidase." J Biol Chem 279(42);43982-9. PMID: 15292190

Maurer05: Maurer LM, Yohannes E, Bondurant SS, Radmacher M, Slonczewski JL (2005). "pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12." J Bacteriol 187(1);304-19. PMID: 15601715

Meisel03: Meisel U, Holtje JV, Vollmer W (2003). "Overproduction of inactive variants of the murein synthase PBP1B causes lysis in Escherichia coli." J Bacteriol 185(18);5342-8. PMID: 12949085

Priyadarshini06: Priyadarshini R, Popham DL, Young KD (2006). "Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli." J Bacteriol 188(15);5345-55. PMID: 16855223

Romeis94a: Romeis T, Holtje JV (1994). "Penicillin-binding protein 7/8 of Escherichia coli is a DD-endopeptidase." Eur J Biochem 224(2);597-604. PMID: 7925376

Scheffers05: Scheffers DJ, Pinho MG (2005). "Bacterial cell wall synthesis: new insights from localization studies." Microbiol Mol Biol Rev 69(4);585-607. PMID: 16339737

Smulski01: Smulski DR, Huang LL, McCluskey MP, Reeve MJ, Vollmer AC, Van Dyk TK, LaRossa RA (2001). "Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12." J Bacteriol 183(11);3353-64. PMID: 11344143

Tomioka78: Tomioka S, Matsuhashi M (1978). "Purification of penicillin-insensitive DD-endopeptidase, a new cell wall peptidoglycan-hydrolyzing enzyme in Escherichia coli, and its inhibition by deoxyribonucleic acids." Biochem Biophys Res Commun 84(4);978-84. PMID: 365181

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vollmer04: Vollmer W, Holtje JV (2004). "The architecture of the murein (peptidoglycan) in gram-negative bacteria: vertical scaffold or horizontal layer(s)?." J Bacteriol 186(18);5978-87. PMID: 15342566

Wei01: Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA (2001). "High-density microarray-mediated gene expression profiling of Escherichia coli." J Bacteriol 183(2);545-56. PMID: 11133948


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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