CSDA_ECOLI
ID CSDA_ECOLI Reviewed; 401 AA.
AC Q46925; Q2MA24;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=Cysteine desulfurase CsdA {ECO:0000303|PubMed:9278392};
DE EC=2.8.1.7 {ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
DE AltName: Full=Cysteine sulfinate desulfinase {ECO:0000303|PubMed:9278392};
DE Short=CSD;
DE EC=3.13.1.- {ECO:0000269|PubMed:9278392};
DE AltName: Full=Selenocysteine lyase {ECO:0000303|PubMed:9278392};
DE EC=4.4.1.16 {ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
GN Name=csdA; Synonyms=ygdJ; OrderedLocusNames=b2810, JW2781;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, AND MUTAGENESIS OF CYS-100; CYS-176 AND CYS-323.
RC STRAIN=K12 / JM109 / ATCC 53323;
RX PubMed=9278392; DOI=10.1074/jbc.272.36.22417;
RA Mihara H., Kurihara T., Yoshimura T., Soda K., Esaki N.;
RT "Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli
RT with selenocysteine lyase and cysteine desulfurase activities. Gene
RT cloning, purification, and characterization of a novel pyridoxal enzyme.";
RL J. Biol. Chem. 272:22417-22424(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Schroeder H., Hauer B.;
RT "Method for producing biotin.";
RL Patent number WO9905285, 04-FEB-1999.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION.
RX PubMed=10829016; DOI=10.1074/jbc.m000926200;
RA Lacourciere G.M., Mihara H., Kurihara T., Esaki N., Stadtman T.C.;
RT "Escherichia coli NifS-like proteins provide selenium in the pathway for
RT the biosynthesis of selenophosphate.";
RL J. Biol. Chem. 275:23769-23773(2000).
RN [6]
RP MUTAGENESIS OF CYS-358, AND ACTIVE SITE CYS-358.
RX PubMed=10739946; DOI=10.1093/oxfordjournals.jbchem.a022641;
RA Mihara H., Kurihara T., Yoshimura T., Esaki N.;
RT "Kinetic and mutational studies of three NifS homologs from Escherichia
RT coli: mechanistic difference between L-cysteine desulfurase and L-
RT selenocysteine lyase reactions.";
RL J. Biochem. 127:559-567(2000).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, INTERACTION
RP WITH CSDE, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15901727; DOI=10.1074/jbc.m504067200;
RA Loiseau L., Ollagnier-de Choudens S., Lascoux D., Forest E., Fontecave M.,
RA Barras F.;
RT "Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S
RT cluster biogenesis in Escherichia coli.";
RL J. Biol. Chem. 280:26760-26769(2005).
RN [8]
RP INDUCTION IN PERSISTER CELLS.
RC STRAIN=K12;
RX PubMed=16768798; DOI=10.1186/1471-2180-6-53;
RA Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K.;
RT "Persisters: a distinct physiological state of E. coli.";
RL BMC Microbiol. 6:53-53(2006).
RN [9]
RP FUNCTION, INTERACTION WITH CSDE, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=20054882; DOI=10.1111/j.1365-2958.2009.06954.x;
RA Trotter V., Vinella D., Loiseau L., Ollagnier de Choudens S., Fontecave M.,
RA Barras F.;
RT "The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf
RT components and participates in a new sulphur transfer pathway by recruiting
RT CsdL (ex-YgdL), a ubiquitin-modifying-like protein.";
RL Mol. Microbiol. 74:1527-1542(2009).
RN [10]
RP FUNCTION, ROLE IN CT(6)A37 FORMATION, AND DISRUPTION PHENOTYPE.
RX PubMed=23242255; DOI=10.1038/nchembio.1137;
RA Miyauchi K., Kimura S., Suzuki T.;
RT "A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed
RT tRNA hypermodification.";
RL Nat. Chem. Biol. 9:105-111(2013).
CC -!- FUNCTION: Catalyzes the removal of elemental sulfur and selenium atoms
CC from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to
CC produce L-alanine, and transiently retains the released sulfur atom on
CC a cysteine residue, in the form of a persulfide. Can also desulfinate
CC L-cysteine sulfinate (3-sulfino-L-alanine), which is the best substrate
CC of the enzyme. Functions as a selenium delivery protein in the pathway
CC for the biosynthesis of selenophosphate. Seems to participate in Fe/S
CC biogenesis by recruiting the SufBCD-SufE proteins. Transfers sulfur to
CC CsdE that increases the cysteine desulfurase activity of CsdA. Can also
CC transfer sulfur directly to TcdA/CsdL in vitro. Appears to support the
CC function of TcdA in the generation of cyclic threonylcarbamoyladenosine
CC at position 37 (ct(6)A37) in tRNAs that read codons beginning with
CC adenine. {ECO:0000269|PubMed:10829016, ECO:0000269|PubMed:15901727,
CC ECO:0000269|PubMed:20054882, ECO:0000269|PubMed:23242255,
CC ECO:0000269|PubMed:9278392}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[sulfur carrier]-H + L-cysteine = [sulfur carrier]-SH + L-
CC alanine; Xref=Rhea:RHEA:43892, Rhea:RHEA-COMP:14737, Rhea:RHEA-
CC COMP:14739, ChEBI:CHEBI:29917, ChEBI:CHEBI:35235, ChEBI:CHEBI:57972,
CC ChEBI:CHEBI:64428; EC=2.8.1.7; Evidence={ECO:0000269|PubMed:15901727,
CC ECO:0000269|PubMed:9278392};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AH2 + L-selenocysteine = A + H(+) + hydrogenselenide + L-
CC alanine; Xref=Rhea:RHEA:11632, ChEBI:CHEBI:13193, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:29317, ChEBI:CHEBI:57843,
CC ChEBI:CHEBI:57972; EC=4.4.1.16;
CC Evidence={ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-sulfino-L-alanine + H2O = H(+) + L-alanine + sulfite;
CC Xref=Rhea:RHEA:28278, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17359, ChEBI:CHEBI:57972, ChEBI:CHEBI:61085;
CC Evidence={ECO:0000269|PubMed:9278392};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
CC -!- ACTIVITY REGULATION: Cysteine desulfurase activity is increased 2-fold
CC in the presence of CsdE. {ECO:0000269|PubMed:15901727}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.24 mM for L-cysteine sulfinate {ECO:0000269|PubMed:9278392};
CC KM=1.0 mM for L-selenocysteine {ECO:0000269|PubMed:9278392};
CC KM=35 mM for L-cysteine {ECO:0000269|PubMed:9278392};
CC KM=3.3 mM for L-cystine {ECO:0000269|PubMed:9278392};
CC Vmax=20 umol/min/mg enzyme with L-cysteine sulfinate as substrate
CC {ECO:0000269|PubMed:9278392};
CC Vmax=7.4 umol/min/mg enzyme with L-selenocysteine as substrate
CC {ECO:0000269|PubMed:9278392};
CC Vmax=3.4 umol/min/mg enzyme with L-cysteine as substrate
CC {ECO:0000269|PubMed:9278392};
CC Vmax=0.017 umol/min/mg enzyme with L-cystine as substrate
CC {ECO:0000269|PubMed:9278392};
CC pH dependence:
CC Optimum pH is around 7.0 and 7.5 for the removal of selenium and
CC sulfur atoms from L-selenocysteine and L-cysteine, respectively.
CC {ECO:0000269|PubMed:9278392};
CC -!- SUBUNIT: Homodimer. Forms a heterodimer with CsdE.
CC {ECO:0000269|PubMed:15901727}.
CC -!- INTERACTION:
CC Q46925; P0AGF2: csdE; NbExp=8; IntAct=EBI-545660, EBI-1130454;
CC Q46925; P15877: gcd; NbExp=2; IntAct=EBI-545660, EBI-545666;
CC Q46925; Q46927: tcdA; NbExp=2; IntAct=EBI-545660, EBI-1130463;
CC -!- INDUCTION: Induced in persister cells. {ECO:0000269|PubMed:16768798}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene display a high decrease
CC in the level of ct(6)A modification in tRNAs, and show the t(6)A
CC modification instead. They also exhibit a fitness defect, are unable to
CC swim, and are more resistant to the norfloxacin antibiotic than the
CC wild-type. {ECO:0000269|PubMed:20054882, ECO:0000269|PubMed:23242255}.
CC -!- SIMILARITY: Belongs to the class-V pyridoxal-phosphate-dependent
CC aminotransferase family. Csd subfamily. {ECO:0000305}.
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DR EMBL; AX000470; CAB77085.1; -; Unassigned_DNA.
DR EMBL; U29581; AAB40460.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75852.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76882.1; -; Genomic_DNA.
DR PIR; F65063; F65063.
DR RefSeq; NP_417290.1; NC_000913.3.
DR RefSeq; WP_001300698.1; NZ_SSUV01000026.1.
DR PDB; 4LW2; X-ray; 1.80 A; A/B/C=1-401.
DR PDB; 4LW4; X-ray; 2.01 A; A/B=1-401.
DR PDB; 5FT4; X-ray; 2.00 A; A/B=1-401.
DR PDB; 5FT5; X-ray; 2.38 A; A/B=1-401.
DR PDB; 5FT6; X-ray; 2.05 A; A/B=1-401.
DR PDB; 5FT8; X-ray; 2.50 A; A/C/E/G/I/K/M/O=1-401.
DR PDBsum; 4LW2; -.
DR PDBsum; 4LW4; -.
DR PDBsum; 5FT4; -.
DR PDBsum; 5FT5; -.
DR PDBsum; 5FT6; -.
DR PDBsum; 5FT8; -.
DR AlphaFoldDB; Q46925; -.
DR SMR; Q46925; -.
DR BioGRID; 4261122; 624.
DR BioGRID; 851605; 2.
DR ComplexPortal; CPX-2137; csdA L-cysteine desulfurase complex.
DR ComplexPortal; CPX-2138; cdsA-cdsE complex.
DR DIP; DIP-9323N; -.
DR IntAct; Q46925; 7.
DR STRING; 511145.b2810; -.
DR jPOST; Q46925; -.
DR PaxDb; Q46925; -.
DR PRIDE; Q46925; -.
DR EnsemblBacteria; AAC75852; AAC75852; b2810.
DR EnsemblBacteria; BAE76882; BAE76882; BAE76882.
DR GeneID; 66673323; -.
DR GeneID; 947275; -.
DR KEGG; ecj:JW2781; -.
DR KEGG; eco:b2810; -.
DR PATRIC; fig|1411691.4.peg.3923; -.
DR EchoBASE; EB2891; -.
DR eggNOG; COG0520; Bacteria.
DR HOGENOM; CLU_003433_2_5_6; -.
DR InParanoid; Q46925; -.
DR OMA; PVCLRYG; -.
DR PhylomeDB; Q46925; -.
DR BioCyc; EcoCyc:G7454-MON; -.
DR BioCyc; MetaCyc:G7454-MON; -.
DR BRENDA; 2.8.1.7; 2026.
DR PRO; PR:Q46925; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1990221; C:L-cysteine desulfurase complex; IPI:ComplexPortal.
DR GO; GO:1990228; C:sulfurtransferase complex; IPI:ComplexPortal.
DR GO; GO:0031071; F:cysteine desulfurase activity; IEA:UniProtKB-EC.
DR GO; GO:0008826; F:cysteine sulfinate desulfinase activity; IEA:RHEA.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR GO; GO:0009000; F:selenocysteine lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0016783; F:sulfurtransferase activity; IDA:EcoCyc.
DR GO; GO:0016226; P:iron-sulfur cluster assembly; IEA:InterPro.
DR GO; GO:0019448; P:L-cysteine catabolic process; IDA:ComplexPortal.
DR GO; GO:0016261; P:selenocysteine catabolic process; IDA:ComplexPortal.
DR GO; GO:0000096; P:sulfur amino acid metabolic process; IDA:EcoCyc.
DR GO; GO:0072348; P:sulfur compound transport; IDA:ComplexPortal.
DR CDD; cd06453; SufS_like; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000192; Aminotrans_V_dom.
DR InterPro; IPR020578; Aminotrans_V_PyrdxlP_BS.
DR InterPro; IPR022471; Cys_desulphurase_CdsA.
DR InterPro; IPR010970; Cys_dSase_SufS.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00266; Aminotran_5; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03392; FeS_syn_CsdA; 1.
DR PROSITE; PS00595; AA_TRANSFER_CLASS_5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Lyase;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..401
FT /note="Cysteine desulfurase CsdA"
FT /id="PRO_0000150291"
FT ACT_SITE 358
FT /note="Cysteine persulfide intermediate"
FT /evidence="ECO:0000305|PubMed:10739946"
FT MOD_RES 222
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT MUTAGEN 100
FT /note="C->A: No loss of activity."
FT /evidence="ECO:0000269|PubMed:9278392"
FT MUTAGEN 176
FT /note="C->A: No loss of activity."
FT /evidence="ECO:0000269|PubMed:9278392"
FT MUTAGEN 323
FT /note="C->A: No loss of activity."
FT /evidence="ECO:0000269|PubMed:9278392"
FT MUTAGEN 358
FT /note="C->A: Loss of cysteine desulfurization."
FT /evidence="ECO:0000269|PubMed:10739946"
FT HELIX 6..10
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 16..19
FT /evidence="ECO:0007829|PDB:4LW2"
FT TURN 25..27
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 33..44
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 55..75
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 84..89
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 90..100
FT /evidence="ECO:0007829|PDB:4LW2"
FT TURN 101..105
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 111..115
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 124..133
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 136..140
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 153..156
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 161..169
FT /evidence="ECO:0007829|PDB:4LW2"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 179..188
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 200..203
FT /evidence="ECO:0007829|PDB:4LW2"
FT TURN 208..212
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 214..219
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 230..234
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 236..241
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 248..256
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 276..289
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 294..312
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 318..320
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 327..333
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 338..347
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:4LW4"
FT HELIX 360..366
FT /evidence="ECO:0007829|PDB:4LW2"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:4LW2"
FT HELIX 382..399
FT /evidence="ECO:0007829|PDB:4LW2"
SQ SEQUENCE 401 AA; 43234 MW; FA30968FE7A9C516 CRC64;
MNVFNPAQFR AQFPALQDAG VYLDSAATAL KPEAVVEATQ QFYSLSAGNV HRSQFAEAQR
LTARYEAARE KVAQLLNAPD DKTIVWTRGT TESINMVAQC YARPRLQPGD EIIVSVAEHH
ANLVPWLMVA QQTGAKVVKL PLNAQRLPDV DLLPELITPR SRILALGQMS NVTGGCPDLA
RAITFAHSAG MVVMVDGAQG AVHFPADVQQ LDIDFYAFSG HKLYGPTGIG VLYGKSELLE
AMSPWLGGGK MVHEVSFDGF TTQSAPWKLE AGTPNVAGVI GLSAALEWLA DYDINQAESW
SRSLATLAED ALAKRPGFRS FRCQDSSLLA FDFAGVHHSD MVTLLAEYGI ALRAGQHCAQ
PLLAELGVTG TLRASFAPYN TKSDVDALVN AVDRALELLV D
