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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)DescriptionActionsGraphical viewLength
Active sitei358Cysteine persulfide intermediate1 Publication1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
Mutagenesisi100C → A: No loss of activity. 1 Publication1
Mutagenesisi176C → A: No loss of activity. 1 Publication1
Mutagenesisi323C → A: No loss of activity. 1 Publication1
Mutagenesisi358C → A: Loss of cysteine desulfurization. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001502911 – 401Cysteine desulfurase CsdAAdd BLAST401

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei222N6-(pyridoxal phosphate)lysineBy similarity1

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 interactors.
DIPiDIP-9323N.
IntActiQ46925. 7 interactors.
STRINGi511145.b2810.

Structurei

Secondary structure

1401
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 10Combined sources5
Helixi16 – 19Combined sources4
Turni25 – 27Combined sources3
Helixi33 – 44Combined sources12
Helixi55 – 75Combined sources21
Helixi81 – 83Combined sources3
Beta strandi84 – 89Combined sources6
Helixi90 – 100Combined sources11
Turni101 – 105Combined sources5
Beta strandi111 – 115Combined sources5
Helixi120 – 122Combined sources3
Helixi124 – 133Combined sources10
Beta strandi136 – 140Combined sources5
Beta strandi146 – 148Combined sources3
Helixi150 – 152Combined sources3
Helixi153 – 156Combined sources4
Beta strandi161 – 169Combined sources9
Turni171 – 173Combined sources3
Helixi179 – 188Combined sources10
Beta strandi192 – 196Combined sources5
Helixi200 – 203Combined sources4
Turni208 – 212Combined sources5
Beta strandi214 – 219Combined sources6
Helixi220 – 222Combined sources3
Beta strandi230 – 234Combined sources5
Helixi236 – 241Combined sources6
Beta strandi248 – 256Combined sources9
Beta strandi259 – 262Combined sources4
Helixi267 – 269Combined sources3
Helixi276 – 289Combined sources14
Helixi294 – 312Combined sources19
Beta strandi318 – 320Combined sources3
Beta strandi327 – 333Combined sources7
Helixi338 – 347Combined sources10
Beta strandi353 – 355Combined sources3
Helixi360 – 366Combined sources7
Beta strandi372 – 375Combined sources4
Helixi382 – 399Combined sources18

3D structure databases

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

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C9B. Bacteria.
COG0520. LUCA.
HOGENOMiHOG000017511.
InParanoidiQ46925.
KOiK01766.
OMAiPYNNQQD.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LW2X-ray1.80A/B/C1-401[»]
4LW4X-ray2.01A/B1-401[»]
ProteinModelPortaliQ46925.
SMRiQ46925.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261122. 584 interactors.
DIPiDIP-9323N.
IntActiQ46925. 7 interactors.
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.
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...

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: November 2, 2016
This is version 139 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.