dcyD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

dcyD

Gene Synonym(s)

yedO, ECK1918, b1919, JW5313[1][2], JW5313

Product Desc.

D-cysteine desulfhydrase[2][3];

Component of DCYSDESULF-CPLX[2]

D-cysteine desulfhydrase; needed for protection from, and utilization of, D-cysteine[4]

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yecC[2]

Regulation/Activity
Quick Links



        

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Notes

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dcyD is a non-essential gene. DcyD is induced under conditions of sulfate limitation. Similar to aminocyclopropane-carboxylate deaminases, but DcyD has no such activity and does not use aminocyclopropane-carboxylate as substrate.[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

dcyD

Mnemonic

Systematic nomenclature

Synonyms

yedO, ECK1918, b1919, JW5313[1][2], JW5313

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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

43.03 minutes 

MG1655: 1997504..1996518
<gbrowseImage> name=NC_000913:1996518..1997504 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1889001..1889987
<gbrowseImage> name=NC_012759:1889001..1889987 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2001617..2000631
<gbrowseImage> name=NC_007779:2000631..2001617 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2088512..2087526
<gbrowseImage> name=NC_010473:2087526..2088512 source=DH10B preset=GeneLocation </gbrowseImage>

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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

1996521

Edman degradation

PMID:11527960


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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

ΔdcyD765::kan

PMID:16738554

CGSC:106156


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

16B12

Kohara Phage

Genobase

PMID:3038334

4B9

Kohara Phage

Genobase

PMID:3038334

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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:G7038

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14038

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003624

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946831

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3792

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006389

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

DcyD[2][1]

Synonyms

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

Product description

D-cysteine desulfhydrase[2][3];

Component of DCYSDESULF-CPLX[2]

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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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 [1].

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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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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<motif_map/>

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

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: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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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

1.86E+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

19.701+/-0.152

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.024340771

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

618

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

795

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

2116

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)

yecC

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Figure courtesy of RegulonDB


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_000913:1997484..1997524 source=MG1655 flip=1 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:b1919 (EcoliWiki Page)

NCBI GEO profiles for dcyD

microarray

GenExpDB:b1919 (EcoliWiki Page)

Summary of data for dcyD 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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<protect>

Notes

Accessions Related to dcyD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7038

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3792

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1919

EcoGene

EcoGene:EG14038

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003624

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006389

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Arabidopsis thaliana

  • AT1G48420 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6ZHE5 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC9223 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YEDO

From SHIGELLACYC

E. coli O157

YEDO

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)

PF00291 Pyridoxal-phosphate dependent enzyme

Panther (EcoliWiki Page)

PTHR10314:SF6

Superfamily (EcoliWiki Page)

SUPERFAMILY:53686

EcoCyc

EcoCyc:G7038

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14038

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

ASAP

ASAP:ABE-0006389

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 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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