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Product(s) |

Expression|

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Standard Name	pbpG
Gene Synonym(s)	ECK2127, b2134, JW5355, yohB^[1], yohB
Product Desc.	penicillin-binding protein 7^[2]^[3] Penicillin-binding proteins PBP7 and PBP8; murein meso-DAP-alanine DD endopeptidase, periplasmic; uniquely binds beta-lactam penems, lysing non-growing cells; mutant has biofilm defect^[4]
Product Synonyms(s)	D-alanyl-D-alanine endopeptidase^[1], B2134^[2]^[1], YohB^[2]^[1], PbpG^[2]^[1] , ECK2127, JW5355, yohB, b2134
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pbpG^[2]
Regulation/Activity
Quick Links
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Notes

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PBP8 is an artifactual OmpT-cleaved proteolytic degradation product of PBP7. PBP7 and PBP8 are also referred to as PBP8a and PBP8b. Earlier conventions had the PBP7 amd PBP8 names reversed.^[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	pbpG
Mnemonic	Penicillin-binding protein
Synonyms	ECK2127, b2134, JW5355, yohB^[1], yohB
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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	47.89 minutes	MG1655: 2222892..2221960 <gbrowseImage> name=NC_000913:2221960..2222892 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2176108..2175176 <gbrowseImage> name=NC_012967:2175176..2176108 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2114443..2115375 <gbrowseImage> name=NC_012759:2114443..2115375 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2228204..2227272 <gbrowseImage> name=NC_007779:2227272..2228204 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2313900..2312968 <gbrowseImage> name=NC_010473:2312968..2313900 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	2221963	Edman degradation	PMID:7721700
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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)	Reference	Availability	Comments
ΔpbpG (Keio:JW5355)	deletion	deletion	PMID:16738554	Shigen CGSC11338^[5]
pbpG::Tn5KAN-2 (FB20635)	Insertion at nt 352 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20635	does not contain pKD46
pbpG::Tn5KAN-2 (FB20636)	Insertion at nt 352 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20636	contains pKD46
ΔpbpG760::kan			PMID:16738554	CGSC:102258
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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
JW5355	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCGAAATTTCGAGTTTCTTT Primer 2:CCATCGTTCTGTGCCGTCTGCCC
1E1	Kohara Phage	Genobase	PMID:3038334
2B2	Kohara Phage	Genobase	PMID:3038334
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: % ^[6] Synonyms:zeg-722, zei-722::Tn10
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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:EG12015	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12015	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001933	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946662	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1952	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007050	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	PbpG
Synonyms	D-alanyl-D-alanine endopeptidase^[1], B2134^[2]^[1], YohB^[2]^[1], PbpG^[2]^[1] , ECK2127, JW5355, yohB, b2134
Product description	penicillin-binding protein 7^[2]^[3] Penicillin-binding proteins PBP7 and PBP8; murein meso-DAP-alanine DD endopeptidase, periplasmic; uniquely binds beta-lactam penems, lysing non-growing cells; mutant has biofilm defect^[4]
EC number (for enzymes)	3.4.99.-^[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:0030288	outer membrane-bounded periplasmic space				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001967	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	P	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: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:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001967	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	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:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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	Notes	References	Evidence
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Notes

Localization

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

Compartment	Evidence	Reference/Source
periplasm
Periplasm	PMID:7721700	EchoLocation:pbpG
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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 MLIMPKFRVS LFSLALMLAV PFAPQAVAKT AAATTASQPE IASGSAMIVD LNTNKVIYSN HPDLVRPIAS ISKLMTAMVV LDARLPLDEK LKVDISQTPE MKGVYSRVRL NSEISRKDML LLALMSSENR AAASLAHHYP GGYKAFIKAM NAKAKSLGMN NTRFVEPTGL SVHNVSTARD LTKLLIASKQ YPLIGQLSTT REDMATFSNP TYTLPFRNTN HLVYRDNWNI QLTKTGFTNA AGHCLVMRTV INNKPVALVV MDAFGKYTHF ADASRLRTWI ETGKVMPVPA AALSYKKQKA AQMAAAGQTA QND
Length	313
Mol. Wt	34.245 kDa
pI	10.4 (calculated)
Extinction coefficient	24,410 - 24,535 (calc based on 9 Y, 2 W, and 1 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
motif	1-25	UniProt Manual:Signal Peptides	UniProt:P0AFI5
Domain	29..262	PF00768 D-alanyl-D-alanine carboxypeptidase		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=pbpG 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:162135905	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946662	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007050	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFI5	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12015	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12015	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946662	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001933	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1952	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	Notes	Reference(s)
Protein	Ecoli K-12	1.067+/-0.225	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.020386266	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	1005	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	242	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	536	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)
pbpG
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Figure courtesy of RegulonDB

</protect>

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_000913:2222872..2222912 source=MG1655 flip=1 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:b2134 (EcoliWiki Page)	NCBI GEO profiles for pbpG
microarray	GenExpDB:b2134 (EcoliWiki Page)	Summary of data for pbpG 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
	GFP Fusion	Intergenic region (2222799..2223103) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:H7^[7]
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Notes

Accessions Related to pbpG Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12015	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1952	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2134
EcoGene	EcoGene:EG12015	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001933	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007050	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	ENSXETP00000007176 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PBPG	From SHIGELLACYC
E. coli O157	PBPG	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:56601
Pfam (EcoliWiki Page)	PF00768 D-alanyl-D-alanine carboxypeptidase
EcoCyc	EcoCyc:EG12015	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12015	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001933	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1952	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007050	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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 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 ^5.2 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pbpG: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 pbpG Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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