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Protein

Cysteine desulfurase CsdA

Gene

csdA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine, and transiently retains the released sulfur atom on a cysteine residue, in the form of a persulfide. Can also desulfinate L-cysteine sulfinate, which is the best substrate of the enzyme. Functions as a selenium delivery protein in the pathway for the biosynthesis of selenophosphate. Seems to participate in Fe/S biogenesis by recruiting the SufBCD-SufE proteins. Transfers sulfur to CsdE that increases the cysteine desulfurase activity of CsdA. Can also transfer sulfur directly to TcdA/CsdL in vitro. Appears to support the function of TcdA in the generation of cyclic threonylcarbamoyladenosine at position 37 (ct6A37) in tRNAs that read codons beginning with adenine.5 Publications

Catalytic activityi

L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor.2 Publications
L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor.2 Publications

Cofactori

pyridoxal 5'-phosphate2 Publications

Enzyme regulationi

Cysteine desulfurase activity is increased 2-fold in the presence of CsdE.1 Publication

Kineticsi

  1. KM=0.24 mM for L-cysteine sulfinate1 Publication
  2. KM=1.0 mM for L-selenocysteine1 Publication
  3. KM=35 mM for L-cysteine1 Publication
  4. KM=3.3 mM for L-cystine1 Publication
  1. Vmax=20 µmol/min/mg enzyme with L-cysteine sulfinate as substrate1 Publication
  2. Vmax=7.4 µmol/min/mg enzyme with L-selenocysteine as substrate1 Publication
  3. Vmax=3.4 µmol/min/mg enzyme with L-cysteine as substrate1 Publication
  4. Vmax=0.017 µmol/min/mg enzyme with L-cystine as substrate1 Publication

pH dependencei

Optimum pH is around 7.0 and 7.5 for the removal of selenium and sulfur atoms from L-selenocysteine and L-cysteine, respectively.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei358 – 3581Cysteine persulfide intermediate1 Publication

GO - Molecular functioni

  • cysteine desulfurase activity Source: UniProtKB-EC
  • pyridoxal phosphate binding Source: EcoCyc
  • selenocysteine lyase activity Source: UniProtKB-EC
  • sulfurtransferase activity Source: EcoCyc

GO - Biological processi

  • iron-sulfur cluster assembly Source: InterPro
  • sulfur amino acid metabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Lyase, Transferase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:G7454-MONOMER.
ECOL316407:JW2781-MONOMER.
MetaCyc:G7454-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cysteine desulfurase CsdA1 Publication (EC:2.8.1.72 Publications)
Alternative name(s):
Cysteine sulfinate desulfinase1 Publication (EC:4.4.1.-)
Short name:
CSD
Selenocysteine lyase1 Publication (EC:4.4.1.162 Publications)
Gene namesi
Name:csdA
Synonyms:ygdJ
Ordered Locus Names:b2810, JW2781
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13082. csdA.

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene display a high decrease in the level of ct6A modification in tRNAs, and show the t6A modification instead. They also exhibit a fitness defect, are unable to swim, and are more resistant to the norfloxacin antibiotic than the wild-type.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi100 – 1001C → A: No loss of activity. 1 Publication
Mutagenesisi176 – 1761C → A: No loss of activity. 1 Publication
Mutagenesisi323 – 3231C → A: No loss of activity. 1 Publication
Mutagenesisi358 – 3581C → A: Loss of cysteine desulfurization. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 401401Cysteine desulfurase CsdAPRO_0000150291Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei222 – 2221N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PaxDbiQ46925.
PRIDEiQ46925.

Expressioni

Inductioni

Induced in persister cells.1 Publication

Interactioni

Subunit structurei

Homodimer. Forms a heterodimer with CsdE.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
csdEP0AGF28EBI-545660,EBI-1130454

Protein-protein interaction databases

BioGridi4261122. 584 interactions.
DIPiDIP-9323N.
IntActiQ46925. 7 interactions.
STRINGi511145.b2810.

Structurei

Secondary structure

1
401
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 105Combined sources
Helixi16 – 194Combined sources
Turni25 – 273Combined sources
Helixi33 – 4412Combined sources
Helixi55 – 7521Combined sources
Helixi81 – 833Combined sources
Beta strandi84 – 896Combined sources
Helixi90 – 10011Combined sources
Turni101 – 1055Combined sources
Beta strandi111 – 1155Combined sources
Helixi120 – 1223Combined sources
Helixi124 – 13310Combined sources
Beta strandi136 – 1405Combined sources
Beta strandi146 – 1483Combined sources
Helixi150 – 1523Combined sources
Helixi153 – 1564Combined sources
Beta strandi161 – 1699Combined sources
Turni171 – 1733Combined sources
Helixi179 – 18810Combined sources
Beta strandi192 – 1965Combined sources
Helixi200 – 2034Combined sources
Turni208 – 2125Combined sources
Beta strandi214 – 2196Combined sources
Helixi220 – 2223Combined sources
Beta strandi230 – 2345Combined sources
Helixi236 – 2416Combined sources
Beta strandi248 – 2569Combined sources
Beta strandi259 – 2624Combined sources
Helixi267 – 2693Combined sources
Helixi276 – 28914Combined sources
Helixi294 – 31219Combined sources
Beta strandi318 – 3203Combined sources
Beta strandi327 – 3337Combined sources
Helixi338 – 34710Combined sources
Beta strandi353 – 3553Combined sources
Helixi360 – 3667Combined sources
Beta strandi372 – 3754Combined sources
Helixi382 – 39918Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LW2X-ray1.80A/B/C1-401[»]
4LW4X-ray2.01A/B1-401[»]
ProteinModelPortaliQ46925.
SMRiQ46925. Positions 2-400.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C9B. Bacteria.
COG0520. LUCA.
HOGENOMiHOG000017511.
InParanoidiQ46925.
KOiK01766.
OMAiPYNNQQD.
OrthoDBiEOG68DD0M.
PhylomeDBiQ46925.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR000192. Aminotrans_V_dom.
IPR020578. Aminotrans_V_PyrdxlP_BS.
IPR022471. Cys_desulphurase_CdsA.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00266. Aminotran_5. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03392. FeS_syn_CsdA. 1 hit.
PROSITEiPS00595. AA_TRANSFER_CLASS_5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q46925-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVFNPAQFR AQFPALQDAG VYLDSAATAL KPEAVVEATQ QFYSLSAGNV
60 70 80 90 100
HRSQFAEAQR LTARYEAARE KVAQLLNAPD DKTIVWTRGT TESINMVAQC
110 120 130 140 150
YARPRLQPGD EIIVSVAEHH ANLVPWLMVA QQTGAKVVKL PLNAQRLPDV
160 170 180 190 200
DLLPELITPR SRILALGQMS NVTGGCPDLA RAITFAHSAG MVVMVDGAQG
210 220 230 240 250
AVHFPADVQQ LDIDFYAFSG HKLYGPTGIG VLYGKSELLE AMSPWLGGGK
260 270 280 290 300
MVHEVSFDGF TTQSAPWKLE AGTPNVAGVI GLSAALEWLA DYDINQAESW
310 320 330 340 350
SRSLATLAED ALAKRPGFRS FRCQDSSLLA FDFAGVHHSD MVTLLAEYGI
360 370 380 390 400
ALRAGQHCAQ PLLAELGVTG TLRASFAPYN TKSDVDALVN AVDRALELLV

D
Length:401
Mass (Da):43,234
Last modified:November 1, 1996 - v1
Checksum:iFA30968FE7A9C516
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AX000470 Unassigned DNA. Translation: CAB77085.1.
U29581 Genomic DNA. Translation: AAB40460.1.
U00096 Genomic DNA. Translation: AAC75852.1.
AP009048 Genomic DNA. Translation: BAE76882.1.
PIRiF65063.
RefSeqiNP_417290.1. NC_000913.3.
WP_001300698.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75852; AAC75852; b2810.
BAE76882; BAE76882; BAE76882.
GeneIDi947275.
KEGGiecj:JW2781.
eco:b2810.
PATRICi32121036. VBIEscCol129921_2910.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AX000470 Unassigned DNA. Translation: CAB77085.1.
U29581 Genomic DNA. Translation: AAB40460.1.
U00096 Genomic DNA. Translation: AAC75852.1.
AP009048 Genomic DNA. Translation: BAE76882.1.
PIRiF65063.
RefSeqiNP_417290.1. NC_000913.3.
WP_001300698.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LW2X-ray1.80A/B/C1-401[»]
4LW4X-ray2.01A/B1-401[»]
ProteinModelPortaliQ46925.
SMRiQ46925. Positions 2-400.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261122. 584 interactions.
DIPiDIP-9323N.
IntActiQ46925. 7 interactions.
STRINGi511145.b2810.

Proteomic databases

PaxDbiQ46925.
PRIDEiQ46925.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75852; AAC75852; b2810.
BAE76882; BAE76882; BAE76882.
GeneIDi947275.
KEGGiecj:JW2781.
eco:b2810.
PATRICi32121036. VBIEscCol129921_2910.

Organism-specific databases

EchoBASEiEB2891.
EcoGeneiEG13082. csdA.

Phylogenomic databases

eggNOGiENOG4105C9B. Bacteria.
COG0520. LUCA.
HOGENOMiHOG000017511.
InParanoidiQ46925.
KOiK01766.
OMAiPYNNQQD.
OrthoDBiEOG68DD0M.
PhylomeDBiQ46925.

Enzyme and pathway databases

BioCyciEcoCyc:G7454-MONOMER.
ECOL316407:JW2781-MONOMER.
MetaCyc:G7454-MONOMER.

Miscellaneous databases

PROiQ46925.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR000192. Aminotrans_V_dom.
IPR020578. Aminotrans_V_PyrdxlP_BS.
IPR022471. Cys_desulphurase_CdsA.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00266. Aminotran_5. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03392. FeS_syn_CsdA. 1 hit.
PROSITEiPS00595. AA_TRANSFER_CLASS_5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme."
    Mihara H., Kurihara T., Yoshimura T., Soda K., Esaki N.
    J. Biol. Chem. 272:22417-22424(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, MUTAGENESIS OF CYS-100; CYS-176 AND CYS-323.
    Strain: K12 / JM109 / ATCC 53323.
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Escherichia coli NifS-like proteins provide selenium in the pathway for the biosynthesis of selenophosphate."
    Lacourciere G.M., Mihara H., Kurihara T., Esaki N., Stadtman T.C.
    J. Biol. Chem. 275:23769-23773(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Kinetic and mutational studies of three NifS homologs from Escherichia coli: mechanistic difference between L-cysteine desulfurase and L-selenocysteine lyase reactions."
    Mihara H., Kurihara T., Yoshimura T., Esaki N.
    J. Biochem. 127:559-567(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-358, ACTIVE SITE CYS-358.
  7. "Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S cluster biogenesis in Escherichia coli."
    Loiseau L., Ollagnier-de Choudens S., Lascoux D., Forest E., Fontecave M., Barras F.
    J. Biol. Chem. 280:26760-26769(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, INTERACTION WITH CSDE, SUBUNIT.
    Strain: K12 / MG1655 / ATCC 47076.
  8. "Persisters: a distinct physiological state of E. coli."
    Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K.
    BMC Microbiol. 6:53-53(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION IN PERSISTER CELLS.
    Strain: K12.
  9. "The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates in a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein."
    Trotter V., Vinella D., Loiseau L., Ollagnier de Choudens S., Fontecave M., Barras F.
    Mol. Microbiol. 74:1527-1542(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CSDE, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  10. "A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification."
    Miyauchi K., Kimura S., Suzuki T.
    Nat. Chem. Biol. 9:105-111(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ROLE IN CT(6)A37 FORMATION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiCSDA_ECOLI
AccessioniPrimary (citable) accession number: Q46925
Secondary accession number(s): Q2MA24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1996
Last modified: January 20, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.