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Product(s) |

Expression|

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Standard Name	mrdA
Gene Synonym(s)	ECK0628, b0635, JW0630, pbpA^[1], pbpA
Product Desc.	cell shape; peptidoglycan synthetase; penicillin-binding protein 2^[2]^[3] Penicillin-binding protein PBP2; transpeptidase recruited by cognate SEDS protein MrdB; mecillinam resistance^[4]
Product Synonyms(s)	transpeptidase involved in peptidoglycan synthesis (penicillin-binding protein 2)^[1], B0635^[2]^[1], PbpA^[2]^[1], MrdA^[2]^[1], PBP2^[2]^[1] , ECK0628, JW0630, pbpA, b0635
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rlpA^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	mrdA
Mnemonic	Murein cluster d
Synonyms	ECK0628, b0635, JW0630, pbpA^[1], pbpA
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	14.34 minutes	MG1655: 667440..665539 <gbrowseImage> name=NC_000913:665539..667440 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 650801..648900 <gbrowseImage> name=NC_012967:648900..650801 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 568299..570200 <gbrowseImage> name=NC_012759:568299..570200 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 668639..666738 <gbrowseImage> name=NC_007779:666738..668639 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 606772..604871 <gbrowseImage> name=NC_010473:604871..606772 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 720032..718131 <gbrowseImage> name=NC_010473:718131..720032 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
pbpA(TS)				PMID:3894330
mrdA1	point mutation	Resistant to	Resistance to mecillinam at 42C. WT at 30C	PMID:6243629	Strain: TMM1	Other strains with same phenotype: TMM2 (mrdA2), TMM3 (mrdA3), TMM5 (mrdA3).
mrdA1		Cell Shape	Spherical cells at 42C. WT rod at 30C.	PMID:6243629	Strain: TMM1	Other strains with same phenotype: TMM2 (mrdA2), TMM3 (mrdA3), TMM5 (mrdA3).
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0630	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACTACAGAACTCTTTTCG Primer 2:CCATGGTCCTCCGCTGCGGCAAC
1G6	Kohara Phage	Genobase	PMID:3038334
15D7	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 68% ^[6] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 24% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10606	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10606	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000599	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945240	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0601	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002178	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	MrdA
Synonyms	transpeptidase involved in peptidoglycan synthesis (penicillin-binding protein 2)^[1], B0635^[2]^[1], PbpA^[2]^[1], MrdA^[2]^[1], PBP2^[2]^[1] , ECK0628, JW0630, pbpA, b0635
Product description	cell shape; peptidoglycan synthetase; penicillin-binding protein 2^[2]^[3] Penicillin-binding protein PBP2; transpeptidase recruited by cognate SEDS protein MrdB; mecillinam resistance^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0071972	peptidoglycan L,D-transpeptidase activity	PMID:6297485	IDA: Inferred from Direct Assay		F	Figure 3 shows peptidoglycan cross-linking in the presence of mrdA.	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008360	regulation of cell shape	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0133	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008658	penicillin binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008658	penicillin binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005311	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009252	peptidoglycan biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0573	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0046	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	PMID:1103132	IMP: Inferred from Mutant Phenotype		P	when Mecillinam was added to non resistant E. Coli, it competed for the same binding site as mrdA.	complete
	GO:0005887	integral to plasma membrane	PMID:1103132	IDA: Inferred from Direct Assay		C	in the sections on penicillin binding protein 2 it is shown that Mecillinam binds exclusively to mrdA in the inner membrane of the cell.	complete
	GO:0008658	penicillin binding	PMID:1103132	IMP: Inferred from Mutant Phenotype		F	Figure 1 shows mrdA binding benzylpenicillin and mecillinam.	complete
	GO:0008360	regulation of cell shape	PMID:1103132	IMP: Inferred from Mutant Phenotype		P	in the B6 mutant, cell shape grew normally when resistant to the Mecillinam antibiotic.	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	tufB	PMID:19402753	MALDI(Z-score):25.144122
Protein	ybgL	PMID:19402753	MALDI(Z-score):30.079097
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKLQNSFRDY TAESALFVRR ALVAFLGILL LTGVLIANLY NLQIVRFTDY QTRSNENRIK LVPIAPSRGI IYDRNGIPLA LNRTIYQIEM MPEKVDNVQQ TLDALRSVVD LTDDDIAAFR KERARSHRFT SIPVKTNLTE VQVARFAVNQ YRFPGVEVKG YKRRYYPYGS ALTHVIGYVS KINDKDVERL NNDGKLANYA ATHDIGKLGI ERYYEDVLHG QTGYEEVEVN NRGRVIRQLK EVPPQAGHDI YLTLDLKLQQ YIETLLAGSR AAVVVTDPRT GGVLALVSTP SYDPNLFVDG ISSKDYSALL NDPNTPLVNR ATQGVYPPAS TVKPYVAVSA LSAGVITRNT TLFDPGWWQL PGSEKRYRDW KKWGHGRLNV TRSLEESADT FFYQVAYDMG IDRLSEWMGK FGYGHYTGID LAEERSGNMP TREWKQKRFK KPWYQGDTIP VGIGQGYWTA TPIQMSKALM ILINDGIVKV PHLLMSTAED GKQVPWVQPH EPPVGDIHSG YWELAKDGMY GVANRPNGTA HKYFASAPYK IAAKSGTAQV FGLKANETYN AHKIAERLRD HKLMTAFAPY NNPQVAVAMI LENGGAGPAV GTLMRQILDH IMLGDNNTDL PAENPAVAAA EDH
Length	633
Mol. Wt	70.857 kDa
pI	9.2 (calculated)
Extinction coefficient	105,660 (calc based on 34 Y, 10 W, and 0 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	271..609	PF00905 Penicillin binding protein transpeptidase domain	PMID:19920124
Domain	63..240	PF03717 Penicillin-binding Protein dimerisation domain	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=mrdA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128618	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945240	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002178	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AD65	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10606	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10606	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945240	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000599	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0601	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	324	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	76	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	148	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
rlpA
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:667420..667460 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0635 (EcoliWiki Page)	NCBI GEO profiles for mrdA
microarray	GenExpDB:b0635 (EcoliWiki Page)	Summary of data for mrdA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to mrdA Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10606	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0601	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0635
EcoGene	EcoGene:EG10606	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000599	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002178	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000000064 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000002897 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	MRDA	From SHIGELLACYC
E. coli O157	MRDA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00905 Penicillin binding protein transpeptidase domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:56519
Superfamily (EcoliWiki Page)	SUPERFAMILY:56601
Pfam (EcoliWiki Page)	PF03717 Penicillin-binding Protein dimerisation domain
EcoCyc	EcoCyc:EG10606	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10606	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000599	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0601	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002178	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

mrdA:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to mrdA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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