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Cysteine desulfurase CsdA (EC 2.8.1.7) (Cysteine sulfinate desulfinase) (CSD) (EC 4.4.1.-) (Selenocysteine lyase) (EC 4.4.1.16)

 CSDA_ECOLI              Reviewed;         401 AA.
Q46925; Q2MA24;
27-APR-2001, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
07-NOV-2018, entry version 150.
RecName: Full=Cysteine desulfurase CsdA {ECO:0000303|PubMed:9278392};
EC=2.8.1.7 {ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
AltName: Full=Cysteine sulfinate desulfinase {ECO:0000303|PubMed:9278392};
Short=CSD;
EC=4.4.1.-;
AltName: Full=Selenocysteine lyase {ECO:0000303|PubMed:9278392};
EC=4.4.1.16 {ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:9278392};
Name=csdA; Synonyms=ygdJ; OrderedLocusNames=b2810, JW2781;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, FUNCTION,
CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
SPECIFICITY, AND MUTAGENESIS OF CYS-100; CYS-176 AND CYS-323.
STRAIN=K12 / JM109 / ATCC 53323;
PubMed=9278392; DOI=10.1074/jbc.272.36.22417;
Mihara H., Kurihara T., Yoshimura T., Soda K., Esaki N.;
"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.";
J. Biol. Chem. 272:22417-22424(1997).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
Schroeder H., Hauer B.;
"Method for producing biotin.";
Patent number WO9905285, 04-FEB-1999.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
FUNCTION.
PubMed=10829016; DOI=10.1074/jbc.M000926200;
Lacourciere G.M., Mihara H., Kurihara T., Esaki N., Stadtman T.C.;
"Escherichia coli NifS-like proteins provide selenium in the pathway
for the biosynthesis of selenophosphate.";
J. Biol. Chem. 275:23769-23773(2000).
[6]
MUTAGENESIS OF CYS-358, AND ACTIVE SITE CYS-358.
PubMed=10739946; DOI=10.1093/oxfordjournals.jbchem.a022641;
Mihara H., Kurihara T., Yoshimura T., Esaki N.;
"Kinetic and mutational studies of three NifS homologs from
Escherichia coli: mechanistic difference between L-cysteine
desulfurase and L-selenocysteine lyase reactions.";
J. Biochem. 127:559-567(2000).
[7]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
INTERACTION WITH CSDE, AND SUBUNIT.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=15901727; DOI=10.1074/jbc.M504067200;
Loiseau L., Ollagnier-de Choudens S., Lascoux D., Forest E.,
Fontecave M., Barras F.;
"Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting
Fe-S cluster biogenesis in Escherichia coli.";
J. Biol. Chem. 280:26760-26769(2005).
[8]
INDUCTION IN PERSISTER CELLS.
STRAIN=K12;
PubMed=16768798; DOI=10.1186/1471-2180-6-53;
Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K.;
"Persisters: a distinct physiological state of E. coli.";
BMC Microbiol. 6:53-53(2006).
[9]
FUNCTION, INTERACTION WITH CSDE, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=20054882; DOI=10.1111/j.1365-2958.2009.06954.x;
Trotter V., Vinella D., Loiseau L., Ollagnier de Choudens S.,
Fontecave M., Barras F.;
"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.";
Mol. Microbiol. 74:1527-1542(2009).
[10]
FUNCTION, ROLE IN CT(6)A37 FORMATION, AND DISRUPTION PHENOTYPE.
PubMed=23242255; DOI=10.1038/nchembio.1137;
Miyauchi K., Kimura S., Suzuki T.;
"A cyclic form of N6-threonylcarbamoyladenosine as a widely
distributed tRNA hypermodification.";
Nat. Chem. Biol. 9:105-111(2013).
-!- FUNCTION: 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 (ct(6)A37) in tRNAs that read codons beginning with
adenine. {ECO:0000269|PubMed:10829016,
ECO:0000269|PubMed:15901727, ECO:0000269|PubMed:20054882,
ECO:0000269|PubMed:23242255, ECO:0000269|PubMed:9278392}.
-!- CATALYTIC ACTIVITY: L-cysteine + acceptor = L-alanine + S-
sulfanyl-acceptor. {ECO:0000269|PubMed:15901727,
ECO:0000269|PubMed:9278392}.
-!- CATALYTIC ACTIVITY: L-selenocysteine + reduced acceptor = selenide
+ L-alanine + acceptor. {ECO:0000269|PubMed:15901727,
ECO:0000269|PubMed:9278392}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000269|PubMed:15901727,
ECO:0000269|PubMed:9278392};
-!- ACTIVITY REGULATION: Cysteine desulfurase activity is increased 2-
fold in the presence of CsdE. {ECO:0000269|PubMed:15901727}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.24 mM for L-cysteine sulfinate
{ECO:0000269|PubMed:9278392};
KM=1.0 mM for L-selenocysteine {ECO:0000269|PubMed:9278392};
KM=35 mM for L-cysteine {ECO:0000269|PubMed:9278392};
KM=3.3 mM for L-cystine {ECO:0000269|PubMed:9278392};
Vmax=20 umol/min/mg enzyme with L-cysteine sulfinate as
substrate {ECO:0000269|PubMed:9278392};
Vmax=7.4 umol/min/mg enzyme with L-selenocysteine as substrate
{ECO:0000269|PubMed:9278392};
Vmax=3.4 umol/min/mg enzyme with L-cysteine as substrate
{ECO:0000269|PubMed:9278392};
Vmax=0.017 umol/min/mg enzyme with L-cystine as substrate
{ECO:0000269|PubMed:9278392};
pH dependence:
Optimum pH is around 7.0 and 7.5 for the removal of selenium and
sulfur atoms from L-selenocysteine and L-cysteine, respectively.
{ECO:0000269|PubMed:9278392};
-!- SUBUNIT: Homodimer. Forms a heterodimer with CsdE.
{ECO:0000269|PubMed:15901727}.
-!- INTERACTION:
P0AGF2:csdE; NbExp=8; IntAct=EBI-545660, EBI-1130454;
P15877:gcd; NbExp=2; IntAct=EBI-545660, EBI-545666;
-!- INDUCTION: Induced in persister cells.
{ECO:0000269|PubMed:16768798}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene display a high
decrease in the level of ct(6)A modification in tRNAs, and show
the t(6)A modification instead. They also exhibit a fitness
defect, are unable to swim, and are more resistant to the
norfloxacin antibiotic than the wild-type.
{ECO:0000269|PubMed:20054882, ECO:0000269|PubMed:23242255}.
-!- SIMILARITY: Belongs to the class-V pyridoxal-phosphate-dependent
aminotransferase family. Csd subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AX000470; CAB77085.1; -; Unassigned_DNA.
EMBL; U29581; AAB40460.1; -; Genomic_DNA.
EMBL; U00096; AAC75852.1; -; Genomic_DNA.
EMBL; AP009048; BAE76882.1; -; Genomic_DNA.
PIR; F65063; F65063.
RefSeq; NP_417290.1; NC_000913.3.
RefSeq; WP_001300698.1; NZ_LN832404.1.
PDB; 4LW2; X-ray; 1.80 A; A/B/C=1-401.
PDB; 4LW4; X-ray; 2.01 A; A/B=1-401.
PDB; 5FT4; X-ray; 2.00 A; A/B=1-401.
PDB; 5FT5; X-ray; 2.38 A; A/B=1-401.
PDB; 5FT6; X-ray; 2.05 A; A/B=1-401.
PDB; 5FT8; X-ray; 2.50 A; A/C/E/G/I/K/M/O=1-401.
PDBsum; 4LW2; -.
PDBsum; 4LW4; -.
PDBsum; 5FT4; -.
PDBsum; 5FT5; -.
PDBsum; 5FT6; -.
PDBsum; 5FT8; -.
ProteinModelPortal; Q46925; -.
SMR; Q46925; -.
BioGrid; 4261122; 624.
ComplexPortal; CPX-2137; CsdA L-cysteine desulfurase complex.
ComplexPortal; CPX-2138; CdsA-CdsE complex.
DIP; DIP-9323N; -.
IntAct; Q46925; 7.
STRING; 316385.ECDH10B_2980; -.
PaxDb; Q46925; -.
PRIDE; Q46925; -.
EnsemblBacteria; AAC75852; AAC75852; b2810.
EnsemblBacteria; BAE76882; BAE76882; BAE76882.
GeneID; 947275; -.
KEGG; ecj:JW2781; -.
KEGG; eco:b2810; -.
PATRIC; fig|1411691.4.peg.3923; -.
EchoBASE; EB2891; -.
EcoGene; EG13082; csdA.
eggNOG; ENOG4105C9B; Bacteria.
eggNOG; COG0520; LUCA.
HOGENOM; HOG000017511; -.
InParanoid; Q46925; -.
KO; K01766; -.
PhylomeDB; Q46925; -.
BioCyc; EcoCyc:G7454-MONOMER; -.
BioCyc; MetaCyc:G7454-MONOMER; -.
PRO; PR:Q46925; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0031071; F:cysteine desulfurase activity; IEA:UniProtKB-EC.
GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
GO; GO:0009000; F:selenocysteine lyase activity; IEA:UniProtKB-EC.
GO; GO:0016783; F:sulfurtransferase activity; IDA:EcoCyc.
GO; GO:0016226; P:iron-sulfur cluster assembly; IEA:InterPro.
GO; GO:0000096; P:sulfur amino acid metabolic process; IDA:EcoCyc.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 1.
InterPro; IPR000192; Aminotrans_V_dom.
InterPro; IPR020578; Aminotrans_V_PyrdxlP_BS.
InterPro; IPR022471; Cys_desulphurase_CdsA.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
Pfam; PF00266; Aminotran_5; 1.
SUPFAM; SSF53383; SSF53383; 1.
TIGRFAMs; TIGR03392; FeS_syn_CsdA; 1.
PROSITE; PS00595; AA_TRANSFER_CLASS_5; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing; Lyase;
Pyridoxal phosphate; Reference proteome; Transferase.
CHAIN 1 401 Cysteine desulfurase CsdA.
/FTId=PRO_0000150291.
ACT_SITE 358 358 Cysteine persulfide intermediate.
{ECO:0000305|PubMed:10739946}.
MOD_RES 222 222 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
MUTAGEN 100 100 C->A: No loss of activity.
{ECO:0000269|PubMed:9278392}.
MUTAGEN 176 176 C->A: No loss of activity.
{ECO:0000269|PubMed:9278392}.
MUTAGEN 323 323 C->A: No loss of activity.
{ECO:0000269|PubMed:9278392}.
MUTAGEN 358 358 C->A: Loss of cysteine desulfurization.
{ECO:0000269|PubMed:10739946}.
HELIX 6 10 {ECO:0000244|PDB:4LW2}.
HELIX 16 19 {ECO:0000244|PDB:4LW2}.
TURN 25 27 {ECO:0000244|PDB:4LW2}.
HELIX 33 44 {ECO:0000244|PDB:4LW2}.
HELIX 55 75 {ECO:0000244|PDB:4LW2}.
HELIX 81 83 {ECO:0000244|PDB:4LW2}.
STRAND 84 89 {ECO:0000244|PDB:4LW2}.
HELIX 90 100 {ECO:0000244|PDB:4LW2}.
TURN 101 105 {ECO:0000244|PDB:4LW2}.
STRAND 111 115 {ECO:0000244|PDB:4LW2}.
HELIX 120 122 {ECO:0000244|PDB:4LW2}.
HELIX 124 133 {ECO:0000244|PDB:4LW2}.
STRAND 136 140 {ECO:0000244|PDB:4LW2}.
STRAND 146 148 {ECO:0000244|PDB:4LW2}.
HELIX 150 152 {ECO:0000244|PDB:4LW2}.
HELIX 153 156 {ECO:0000244|PDB:4LW2}.
STRAND 161 169 {ECO:0000244|PDB:4LW2}.
TURN 171 173 {ECO:0000244|PDB:4LW2}.
HELIX 179 188 {ECO:0000244|PDB:4LW2}.
STRAND 192 196 {ECO:0000244|PDB:4LW2}.
HELIX 200 203 {ECO:0000244|PDB:4LW2}.
TURN 208 212 {ECO:0000244|PDB:4LW2}.
STRAND 214 219 {ECO:0000244|PDB:4LW2}.
HELIX 220 222 {ECO:0000244|PDB:4LW2}.
STRAND 230 234 {ECO:0000244|PDB:4LW2}.
HELIX 236 241 {ECO:0000244|PDB:4LW2}.
STRAND 248 256 {ECO:0000244|PDB:4LW2}.
STRAND 259 262 {ECO:0000244|PDB:4LW2}.
HELIX 267 269 {ECO:0000244|PDB:4LW2}.
HELIX 276 289 {ECO:0000244|PDB:4LW2}.
HELIX 294 312 {ECO:0000244|PDB:4LW2}.
STRAND 318 320 {ECO:0000244|PDB:4LW2}.
STRAND 327 333 {ECO:0000244|PDB:4LW2}.
HELIX 338 347 {ECO:0000244|PDB:4LW2}.
STRAND 353 355 {ECO:0000244|PDB:4LW4}.
HELIX 360 366 {ECO:0000244|PDB:4LW2}.
STRAND 372 375 {ECO:0000244|PDB:4LW2}.
HELIX 382 399 {ECO:0000244|PDB:4LW2}.
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


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