cspD:Gene Product(s): Difference between revisions

Standard name	CspD
Synonyms	cold shock protein homolog^[1], B0880^[2]^[1], YbjA^[2]^[1], CspD^[2]^[1]
Product description	DNA replication inhibitor^[2]^[3]; Component of cold shock protein homolog^[3] Inhibitor of DNA replication; cold shock protein homolog, not cold shock inducible; stationary phase and starvation inducible; lethal when overproduced^[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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011129	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012156	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012751	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002059	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	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:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012751	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:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002059	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012751	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006950	response to stress	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012751	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008156	negative regulation of DNA replication	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0236	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003697	single-stranded DNA binding	PMID:11260474^[5]	IDA: Inferred from Direct Assay		F	Figure 4	complete
	GO:0042594	response to starvation	PMID:9260955^[6]	IDA: Inferred from Direct Assay		P	Figure 4	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
Protein	Subunits of cold shock protein homolog	could be indirect
Protein	aceE		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	cspC		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767, EBI-883980
Protein	cspE		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	deaD		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	pnp		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rho		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rplA		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rplB		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rplC		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767
Protein	rpsA		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rpsB		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767
Protein	rpsC		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rpsE		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767
Protein	rpsG		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767
Protein	rpsM		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	tehB		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rnr		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	ycbY		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rluC		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rluB		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	accA		PMID:15690043^[7]	Experiment(s):EBI-879539
Protein	rpsD		PMID:15690043^[7]	Experiment(s):EBI-879539, EBI-883767
Protein	acrD		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	aspA		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	ddpB		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	ddlA		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	dppD		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	skp		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	hupA		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rplM		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rplS		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rplX		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rpsJ		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rpsN		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rpsT		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rpsU		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	ydiA		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	yfiF		PMID:15690043^[7]	Experiment(s):EBI-883767
Protein	rho		PMID:19402753^[8]	MALDI(Z-score):37.446310
Protein	ddlA		PMID:19402753^[8]	LCMS(ID Probability):99.0
Protein	rpsJ		PMID:19402753^[8]	LCMS(ID Probability):99.6 MALDI(Z-score):5.368742
Protein	skp		PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rpsN		PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rpsT		PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rpsA		PMID:19402753^[8]	MALDI(Z-score):24.834488
Protein	rplS		PMID:19402753^[8]	LCMS(ID Probability):99.0 MALDI(Z-score):4.578737
Protein	rpsU		PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rplM		PMID:19402753^[8]	LCMS(ID Probability):99.6 MALDI(Z-score):5.962325
Protein	rpsC		PMID:19402753^[8]	MALDI(Z-score):25.075789
Protein	aspA		PMID:19402753^[8]	LCMS(ID Probability):99.0
Protein	rpsM		PMID:19402753^[8]	MALDI(Z-score):26.386877
Protein	rplX		PMID:19402753^[8]	LCMS(ID Probability):99.6
Protein	rplB		PMID:19402753^[8]	MALDI(Z-score):29.727578
Protein	rpsD		PMID:19402753^[8]	LCMS(ID Probability):99.0 MALDI(Z-score):35.563879
Protein	ppsR		PMID:19402753^[8]	LCMS(ID Probability):99.0
Protein	rplA		PMID:19402753^[8]	LCMS(ID Probability):95.4 MALDI(Z-score):31.394353
Protein	rlmL		PMID:19402753^[8]	MALDI(Z-score):20.841640
Protein	acrD		PMID:19402753^[8]	LCMS(ID Probability):99.0
Protein	cspE		PMID:19402753^[8]	LCMS(ID Probability):97.9 MALDI(Z-score):17.053160
Protein	yfiF		PMID:19402753^[8]	LCMS(ID Probability):99.0 MALDI(Z-score):19.466810
Protein	rnr		PMID:19402753^[8]	MALDI(Z-score):23.323615
Protein	rluC		PMID:19402753^[8]	MALDI(Z-score):26.672161
Protein	deaD		PMID:19402753^[8]	MALDI(Z-score):25.179680
Protein	rluB		PMID:19402753^[8]	MALDI(Z-score):35.756062
Protein	cspC		PMID:19402753^[8]	LCMS(ID Probability):99.6 MALDI(Z-score):17.053160
Protein	dppD		PMID:19402753^[8]	LCMS(ID Probability):99.0
Protein	ddpB		PMID:19402753^[8]	LCMS(ID Probability):99.0
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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	Source	Notes
Nucleoid			PMID:11520610^[9]
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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 MEKGTVKWFN NAKGFGFICP EGGGEDIFAH YSTIQMDGYR TLKAGQSVQF DVHQGPKGNH ASVIVPVEVE AAVA
Length
Mol. Wt
pI
Extinction coefficient
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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
Domain	1..67	PF00313 'Cold-shock' DNA-binding domain		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=cspD taxon=562,83333 </beststructure>

Models

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Structure figures

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
EcoCyc (EcoliWiki Page)	EcoCyc:EG11111-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P0A968
UniProt (EcoliWiki Page)	UniProt:P0A968
PFAM (EcoliWiki Page)	Pfam:P0A968
RefSeq (EcoliWiki Page)	RefSeq:NP_415401
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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 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 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
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Yamanaka, K et al. (2001) CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli. Mol. Microbiol. 39 1572-84 PubMed
↑ Yamanaka, K & Inouye, M (1997) Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli. J. Bacteriol. 179 5126-30 PubMed
↑ ^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 ^7.24 ^7.25 ^7.26 ^7.27 ^7.28 ^7.29 ^7.30 ^7.31 ^7.32 ^7.33 ^7.34 ^7.35 ^7.36 ^7.37 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^8.00 ^8.01 ^8.02 ^8.03 ^8.04 ^8.05 ^8.06 ^8.07 ^8.08 ^8.09 ^8.10 ^8.11 ^8.12 ^8.13 ^8.14 ^8.15 ^8.16 ^8.17 ^8.18 ^8.19 ^8.20 ^8.21 ^8.22 ^8.23 ^8.24 ^8.25 ^8.26 ^8.27 ^8.28 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Giangrossi, M et al. (2001) Different in vivo localization of the Escherichia coli proteins CspD and CspA. FEMS Microbiol. Lett. 202 171-6 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

@@ Line 1,277: / Line 1,277: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P0A968 Protein Model Portal]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
 * [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
-* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
 * [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)

cspD:Gene Product(s): Difference between revisions

Revision as of 16:08, 17 August 2011

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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cspD:Gene Product(s): Difference between revisions

Revision as of 16:08, 17 August 2011

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

Search