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On One Page

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Gene |

Product(s) |

Expression|

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References |

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Standard Name	smpB
Gene Synonym(s)	ECK2616, b2620, JW2601, smqB^[1], smqB
Product Desc.	small protein B^[2]^[3] tmRNA RNA-binding protein; required for peptide-tagging trans-translation and association of tmRNA(SsrA) with ribosomes^[4]
Product Synonyms(s)	trans-translation protein^[1], B2620^[2]^[1], SmqB^[2]^[1], SmpB^[2]^[1] , ECK2616, JW2601, smqB, b2620
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): smpB^[2]
Regulation/Activity
Quick Links
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Notes

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otherPDB (A. aeolicus): 1P6V; 1K8H. otherPDB (T. thermophilus): 2OB7; 1J1H.^[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	smpB
Mnemonic	Small protein
Synonyms	ECK2616, b2620, JW2601, smqB^[1], smqB
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Notes

Location(s) and DNA Sequence

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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	59.33 minutes	MG1655: 2752918..2753400 <gbrowseImage> name=NC_000913:2752918..2753400 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2676191..2676673 <gbrowseImage> name=NC_012967:2676191..2676673 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2638730..2639212 <gbrowseImage> name=NC_012759:2638730..2639212 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2753552..2754034 <gbrowseImage> name=NC_007779:2753552..2754034 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2844683..2845165 <gbrowseImage> name=NC_010473:2844683..2845165 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	2752921	Edman degradation	PMID:2045357 PMID:10393194
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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
ΔsmpB (Keio:JW2601)	deletion	deletion	PMID:16738554	Shigen CGSC10058^[5]
smpB::Tn5KAN-I-SceI (FB20867)	Insertion at nt 256 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20867	does not contain pKD46
smpB::Tn5KAN-I-SceI (FB20868)	Insertion at nt 256 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20868	contains pKD46
ΔsmpB776::kan			PMID:16738554	CGSC:102976
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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
JW2601	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGAAGAAAAAAGCACATAA Primer 2:CCACGGTGGGCGTTTTTCATGAT
E8F2	Kohara Phage	Genobase	PMID:3038334
22D7	Kohara Phage	Genobase	PMID:3038334
24G1	Kohara Phage	Genobase	PMID:3038334
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 58% ^[6]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::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:EG11782	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11782	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001716	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947296	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1730	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008622	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	SmpB
Synonyms	trans-translation protein^[1], B2620^[2]^[1], SmqB^[2]^[1], SmpB^[2]^[1] , ECK2616, JW2601, smqB, b2620
Product description	small protein B^[2]^[3] tmRNA RNA-binding protein; required for peptide-tagging trans-translation and association of tmRNA(SsrA) with ribosomes^[4]
EC number (for enzymes)
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Notes

Function

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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:0003723	RNA binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00023	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000037	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00023	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:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000037	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	aidB	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	clpA	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	infB	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	malP	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	parC	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	rplF	PMID:15690043^[7]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsA	PMID:15690043^[7]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsB	PMID:15690043^[7]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsC	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	secA	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	selB	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	ycbB	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	yfiF	PMID:15690043^[7]	Experiment(s):EBI-882920
Protein	gyrA	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	gyrB	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	skp	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	hupA	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	hupB	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	rplM	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	rplX	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	rpmB	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	rpsE	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	rpsN	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	yeeX	PMID:15690043^[7]	Experiment(s):EBI-890426
Protein	vsr	PMID:16606699^[8]	Experiment(s):EBI-1143521
Protein	yibK	PMID:16606699^[8]	Experiment(s):EBI-1143521
Protein	rplA	PMID:16606699^[8]	Experiment(s):EBI-1143521
Protein	ycgE	PMID:16606699^[8]	Experiment(s):EBI-1143521
Protein	ycfJ	PMID:16606699^[8]	Experiment(s):EBI-1143521
Protein	secA	PMID:19402753^[9]	MALDI(Z-score):18.851547
Protein	aidB	PMID:19402753^[9]	LCMS(ID Probability):98.3 MALDI(Z-score):27.388524
Protein	rplF	PMID:19402753^[9]	LCMS(ID Probability):99.6 MALDI(Z-score):35.816231
Protein	skp	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	rpsA	PMID:19402753^[9]	LCMS(ID Probability):99.6 MALDI(Z-score):26.098127
Protein	gyrA	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	parC	PMID:19402753^[9]	MALDI(Z-score):37.105392
Protein	malP	PMID:19402753^[9]	MALDI(Z-score):28.886498
Protein	clpA	PMID:19402753^[9]	MALDI(Z-score):25.712309
Protein	hupB	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	rpsN	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	gyrB	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	hupA	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	yfiF	PMID:19402753^[9]	MALDI(Z-score):36.128347
Protein	rplM	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	yeeX	PMID:19402753^[9]	LCMS(ID Probability):99.6
Protein	ycbB	PMID:19402753^[9]	MALDI(Z-score):24.925478
RNA	SsrA RNA
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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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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 MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN ISDSYVLLRD GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL YGRVNREGYT VVALSLYWKN AWCKVKIGVA KGKKQHDKRS DIKEREWQVD KARIMKNAHR
Length	160
Mol. Wt	18.269 kDa
pI	10.4 (calculated)
Extinction coefficient	29,450 - 29,700 (calc based on 5 Y, 4 W, and 2 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:P0A832
Domain	12..80	PF01668 SmpB protein		PMID:19920124^[10]
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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=smpB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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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:16130539	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947296	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008622	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A832	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11782	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11782	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947296	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001716	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1730	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	E. coli K-12 MC4100	7.63E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	14.608+/-0.098	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.079875519	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	4934	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	1537	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	2942	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)
smpB
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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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<gbrowseImage> name=NC_000913:2752898..2752938 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

</protect>

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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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:b2620 (EcoliWiki Page)	NCBI GEO profiles for smpB
microarray	GenExpDB:b2620 (EcoliWiki Page)	Summary of data for smpB 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 (2752705..2752941) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:D10^[11]
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Notes

Accessions Related to smpB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11782	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1730	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2620
EcoGene	EcoGene:EG11782	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001716	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008622	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	ENSXETP00000015164 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	SMPB	From SHIGELLACYC
E. coli O157	SMPB	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:74982
Pfam (EcoliWiki Page)	PF01668 SmpB protein
PFAM (EcoliWiki Page)	PFAM:PF01668
EcoCyc	EcoCyc:EG11782	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11782	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001716	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1730	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008622	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 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).
↑ ^7.00 ^7.01 ^7.02 ^7.03 ^7.04 ^7.05 ^7.06 ^7.07 ^7.08 ^7.09 ^7.10 ^7.11 ^7.12 ^7.13 ^7.14 ^7.15 ^7.16 ^7.17 ^7.18 ^7.19 ^7.20 ^7.21 ^7.22 ^7.23 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^9.00 ^9.01 ^9.02 ^9.03 ^9.04 ^9.05 ^9.06 ^9.07 ^9.08 ^9.09 ^9.10 ^9.11 ^9.12 ^9.13 ^9.14 ^9.15 ^9.16 ^9.17 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

smpB: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 smpB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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