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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	murD
Gene Synonym(s)	ECK0089, b0088, JW0086^[1], JW0086
Product Desc.	UDP-NACMURALA-GLU-LIG^[2]^[3] D-glutamic acid adding enzyme; UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase^[4]
Product Synonyms(s)	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase^[1], B0088^[2]^[1], MurD^[2]^[1] , ECK0089, JW0086, b0088
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ^[2]
Regulation/Activity
Quick Links
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Notes

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A carbamylated lysine residue is present in the active site. MurD also catalyses the synthesis of adenosine 5'-tetraphosphate.^[4]

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	murD
Mnemonic	Murein
Synonyms	ECK0089, b0088, JW0086^[1], JW0086
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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	2.09 minutes	MG1655: 97087..98403 <gbrowseImage> name=NC_000913:97087..98403 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 99891..101207 <gbrowseImage> name=NC_012967:99891..101207 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 97086..98402 <gbrowseImage> name=NC_012759:97086..98402 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 97087..98403 <gbrowseImage> name=NC_007779:97087..98403 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 71191..72507 <gbrowseImage> name=NC_010473:71191..72507 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
Coding Start (SO:0000323)	MG1655	97090	Edman degradation	PMID:1765076
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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)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
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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
JW0086	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTGATTATCAGGGTAAAAA Primer 2:CCACCTAACTCCTTCGCCAGACG
6F3	Kohara Phage	Genobase	PMID:3038334
15B8	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 62% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 9% ^[6]
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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:EG10620	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10620	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944818	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000613	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0615	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000318	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	MurD
Synonyms	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase^[1], B0088^[2]^[1], MurD^[2]^[1] , ECK0089, JW0086, b0088
Product description	UDP-NACMURALA-GLU-LIG^[2]^[3] D-glutamic acid adding enzyme; UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase^[4]
EC number (for enzymes)	6.3.2.9^[1]
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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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00639	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004101	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013221	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00639	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0007047	cellular cell wall organization	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0961	P	Seeded from EcoCyc (v14.0)	complete
	GO:0007049	cell cycle	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0131	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008360	regulation of cell shape	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	P	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:0008764	UDP-N-acetylmuramoylalanine-D-glutamate ligase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00639	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008764	UDP-N-acetylmuramoylalanine-D-glutamate ligase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008764	UDP-N-acetylmuramoylalanine-D-glutamate ligase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:6.3.2.9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:1765076	IDA: Inferred from Direct Assay		C		complete
	GO:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004101	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009058	biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013221	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009252	peptidoglycan biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00639	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009252	peptidoglycan biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	P	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:0051301	cell division	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005762	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051301	cell division	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0132	P	Seeded from EcoCyc (v14.0)	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	aegA	PMID:15690043	Experiment(s):EBI-894076
Protein	yrfB	PMID:15690043	Experiment(s):EBI-894076
Protein	slyD	PMID:16606699	Experiment(s):EBI-1135545
Protein	aegA	PMID:19402753	LCMS(ID Probability):99.6
Protein	hofO	PMID:19402753	LCMS(ID Probability):99.6
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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
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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 MADYQGKNVV IIGLGLTGLS CVDFFLARGV TPRVMDTRMT PPGLDKLPEA VERHTGSLND EWLMAADLIV ASPGIALAHP SLSAAADAGI EIVGDIELFC REAQAPIVAI TGSNGKSTVT TLVGEMAKAA GVNVGVGGNI GLPALMLLDD ECELYVLELS SFQLETTSSL QAVAATILNV TEDHMDRYPF GLQQYRAAKL RIYENAKVCV VNADDALTMP IRGADERCVS FGVNMGDYHL NHQQGETWLR VKGEKVLNVK EMKLSGQHNY TNALAALALA DAAGLPRASS LKALTTFTGL PHRFEVVLEH NGVRWINDSK ATNVGSTEAA LNGLHVDGTL HLLLGGDGKS ADFSPLARYL NGDNVRLYCF GRDGAQLAAL RPEVAEQTET MEQAMRLLAP RVQPGDMVLL SPACASLDQF KNFEQRGNEF ARLAKELG
Length	438
Mol. Wt	46.973 kDa
pI	5.1 (calculated)
Extinction coefficient	29,910 - 30,785 (calc based on 9 Y, 3 W, and 7 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	Notes	References
Initiator Methionine	1	Removed	UniProt:P14900
Domain	300..379	PF02875 Mur ligase family, glutamate ligase domain		PMID:19920124
Domain	110..280	PF08245 Mur ligase middle 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=murD 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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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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
NCBI (Protein) (EcoliWiki Page)	GI:16128081	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944818	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000318	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P14900	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10620	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10620	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944818	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000613	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0615	Escherichia coli str. K-12 substr. MG1655
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Notes

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	885	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	394	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	872	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)
mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ
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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_000913:97067..97107 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b0088 (EcoliWiki Page)	NCBI GEO profiles for murD
microarray	GenExpDB:b0088 (EcoliWiki Page)	Summary of data for murD 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 murD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10620	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0615	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0088
EcoGene	EcoGene:EG10620	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000613	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000318	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
Xenopus tropicalis	ENSXETP00000038518 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	MURD	From SHIGELLACYC
E. coli O157	MURD	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)	PF02875 Mur ligase family, glutamate ligase domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51984
Panther (EcoliWiki Page)	PTHR23135:SF2
Superfamily (EcoliWiki Page)	SUPERFAMILY:53244
Superfamily (EcoliWiki Page)	SUPERFAMILY:53623
Pfam (EcoliWiki Page)	PF08245 Mur ligase middle domain
EcoCyc	EcoCyc:EG10620	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10620	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000613	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0615	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000318	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 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 ^4.2 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).

murD:On One Page

Quickview

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 murD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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