dcyD:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

DcyD[1][2]

Synonyms

D-cysteine desulfhydrase, PLP-dependent[2], YedO[1][2], B1919[1][2], YedO , ECK1918, JW5313, yedO, b1919

Product description

D-cysteine desulfhydrase[1][3];

Component of DCYSDESULF-CPLX[1]

D-cysteine desulfhydrase; needed for protection from, and utilization of, D-cysteine[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [2].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001926

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005966

F

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0019148

D-cysteine desulfhydrase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01045

F

Seeded from EcoCyc (v14.0)

complete

GO:0019148

D-cysteine desulfhydrase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.4.1.15

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001926

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005966

F

Seeded from EcoCyc (v14.0)

complete

GO:0046416

D-amino acid metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01045

P

Seeded from EcoCyc (v14.0)

complete

GO:0046416

D-amino acid metabolic process

PMID:11527960[5]

IDA: Inferred from Direct Assay

P

complete

GO:0019148

D-cysteine desulfhydrase activity

PMID:11527960[5]

IDA: Inferred from Direct Assay

F

complete

GO:0006950

response to stress

PMID:11527960[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006790

sulfur metabolic process

PMID:11527960[5]

IDA: Inferred from Direct Assay

P

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 DCYSDESULF-CPLX

could be indirect

Protein

rplA

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

rplC

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

rpsC

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

rpsD

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

rpsE

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

sucB

PMID:15690043[6]

Experiment(s):EBI-880545, EBI-880739, EBI-886398

Protein

rplD

PMID:15690043[6]

Experiment(s):EBI-880545

Protein

ttdR

PMID:15690043[6]

Experiment(s):EBI-886398

Protein

rpsL

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsI

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsS

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):2.166556

Protein

rpsU

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753[7]

LCMS(ID Probability):98.0 MALDI(Z-score):23.030424

Protein

rpsC

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):28.300772

Protein

rplA

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):28.483978

Protein

sucB

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):38.384781

Protein

rplD

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):13.322206

Protein

yeeX

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):4.976451

Protein

ttdR

PMID:19402753[7]

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

cytoplasm

From EcoCyc[3]


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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 

MTKKGAFTSA FFIYAFSACI IRKSQQHTSE AVMPLHNLTR FPRLEFIGAP TPLEYLPRFS
DYLGREIFIK RDDVTPMAMG GNKLRKLEFL AADALREGAD TLITAGAIQS NHVRQTAAVA
AKLGLHCVAL LENPIGTTAE NYLTNGNRLL LDLFNTQIEM CDALTDPNAQ LEELATRVEA
QGFRPYVIPV GGSNALGALG YVESALEIAQ QCEGAVNISS VVVASGSAGT HAGLAVGLEH
LMPESELIGV TVSRSVADQL PKVVNLQQAI AKELELTASA EILLWDDYFA PGYGVPNDEG
MEAVKLLARL EGILLDPVYT GKAMAGLIDG ISQKRFKDEG PILFIHTGGA PALFAYHPHV
Length

360

Mol. Wt

38.706 kDa

pI

5.2 (calculated)

Extinction coefficient

20,400 - 20,900 (calc based on 10 Y, 1 W, and 4 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:P76316

Domain

12..316

PF00291 Pyridoxal-phosphate dependent enzyme

PMID:19920124[8]

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

Structures

<beststructure> gene=dcyD 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:90111355

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946831

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006389

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76316

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7038

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14038

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946831

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003624

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3792

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.0 1.1 1.2 1.3 1.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 5.3 Soutourina, J et al. (2001) Role of D-cysteine desulfhydrase in the adaptation of Escherichia coli to D-cysteine. J. Biol. Chem. 276 40864-72 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 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 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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