EzCatDB: D00659
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DB codeD00659
CATH domainDomain 13.90.1150.10 : Aspartate Aminotransferase, domain 1Catalytic domain
Domain 23.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
E.C.2.8.1.7
CSA1ecx


Enzyme Name
UniProtKBKEGG

P0A6B7P0A6B9Q9X218Q55793
Protein nameCysteine desulfuraseCysteine desulfurase
Probable cysteine desulfuraseCysteine desulfurase
IscS
NIFS
NifS
SufS
Cysteine desulfurylase
SynonymsEC 2.8.1.7
NifS protein homolog
ThiI transpersulfidase
EC 2.8.1.7
Aminotransferase, class V
Cysteine desulfurase
EC 2.8.1.7
EC 2.8.1.7
RefSeqYP_026169.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490758.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_289087.1 (Protein)
NC_002655.2 (DNA/RNA sequence)
NP_311423.2 (Protein)
NC_002695.1 (DNA/RNA sequence)
NP_229492.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
NP_442475.1 (Protein)
NC_000911.1 (DNA/RNA sequence)
YP_005652536.1 (Protein)
NC_017277.1 (DNA/RNA sequence)
YP_007452351.1 (Protein)
NC_020286.1 (DNA/RNA sequence)
PfamPF00266 (Aminotran_5)
[Graphical view]
PF00266 (Aminotran_5)
[Graphical view]
PF00266 (Aminotran_5)
[Graphical view]
PF00266 (Aminotran_5)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00730Thiamine metabolism

UniProtKB:Accession NumberP0A6B7P0A6B9Q9X218Q55793
Entry nameISCS_ECOLIISCS_ECO57Q9X218_THEMACSD_SYNY3
ActivityL-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor.L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor
L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor.
SubunitHomodimer. The homodimer interacts with tusA.


Subcellular locationCytoplasm (Probable).


CofactorPyridoxal phosphate.Pyridoxal phosphate.Pyridoxal phosphate.Pyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C00097L00106C00041L00105I00165I00166I00167I00171C15812I00030I00032I00049
CompoundPyridoxal phosphateL-cysteineAcceptor for sulfurL-alanineS-sulfanyl-acceptorExternal aldimine intermediate (PLP-L-Cys)Quinonoid intermediate (PLP-Cys)Ketimine intermediate (PLP-Cys)Aminoacrylate intermediate (PLP-dehydroAla)[enzyme]-S-sulfanylcysteineKetimine intermediate (PLP-Ala)Quinonoid intermediate (PLP-Ala)External aldimine intermediate (PLP-L-Ala)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamino acids,sulfhydryl groupothersamino acidsothers,sulfhydryl group







ChEBI18405
17561
35235

16977
57972









PubChem1051
6419722
5862

7311724
5950









                     
1p3wA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1p3wB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvjA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvjB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvkA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvlB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvmA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvmB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ecxA01UnboundBound:CYS 502UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ecxB01UnboundBound:CYS 503UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eg5A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eg5B01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1t3iA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1t3iB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1p3wA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1p3wB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvjA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvjB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvkA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvlB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvmA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3lvmB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ecxA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ecxB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eg5A02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eg5B02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1t3iA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1t3iB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature[3],[8],[9]
pdbCatalytic residuesCofactor-binding residuescomment
           
1p3wA01       
 
invisible 328-333
1p3wB01       
 
invisible 328-333
3lvjA01       
 
invisible 327-332
3lvjB01CYS 328
 
invisible 329-332
3lvkA01CYS 328
 
invisible 329-332
3lvlB01       
 
invisible 328-332
3lvmA01       
 
invisible 328-332
3lvmB01       
 
invisible 328-332
1ecxA01       
 
invisible 321-332
1ecxB01       
 
invisible 321-331
1eg5A01       
 
invisible 321-332
1eg5B01       
 
invisible 321-331
1t3iA01CYS 372
 
 
1t3iB01CYS 372
 
 
1p3wA02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
1p3wB02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvjA02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvjB02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvkA02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvlB02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvmA02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
3lvmB02HIS 104;ASP 180;GLN 183;LYS 206
LYS 206(PLP binding)
 
1ecxA02HIS  99;ASP 177;GLN 180;LYS 203
LYS 203(PLP binding)
 
1ecxB02HIS  99;ASP 177;GLN 180;LYS 203
LYS 203(PLP binding)
 
1eg5A02HIS  99;ASP 177;GLN 180;LYS 203
LYS 203(PLP binding)
 
1eg5B02HIS  99;ASP 177;GLN 180;LYS 203
LYS 203(PLP binding)
 
1t3iA02HIS 128;ASP 205;GLN 208;LYS 231
LYS 231(PLP binding)
 
1t3iB02HIS 128;ASP 205;GLN 208;LYS 231
LYS 231(PLP binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]SCHEME3, p.4719
[3]SCHEME1, p.459-460

references
[1]
PubMed ID8161529
JournalBiochemistry
Year1994
Volume33
Pages4714-20
AuthorsZheng L, White RH, Cash VL, Dean DR
TitleMechanism for the desulfurization of L-cysteine catalyzed by the nifS gene product.
[2]
CommentsPROTEIN SEQUENCE OF 1-9, MUTAGENESIS OF CYS-328.
PubMed ID10739946
JournalJ Biochem
Year2000
Volume127
Pages559-67
AuthorsMihara H, Kurihara T, Yoshimura T, Esaki N
TitleKinetic and mutational studies of three NifS homologs from Escherichia coli: mechanistic difference between L-cysteine desulfurase and L-selenocysteine lyase reactions.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), ACTIVE SITE, AND PYRIDOXAL PHOSPHATE AT LYS-203.
PubMed ID10715213
JournalJ Mol Biol
Year2000
Volume297
Pages451-64
AuthorsKaiser JT, Clausen T, Bourenkow GP, Bartunik HD, Steinbacher S, Huber R
TitleCrystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
Related PDB1ecx,1eg5
[4]
PubMed ID11577100
JournalJ Biol Chem
Year2001
Volume276
Pages44521-6
AuthorsUrbina HD, Silberg JJ, Hoff KG, Vickery LE
TitleTransfer of sulfur from IscS to IscU during Fe/S cluster assembly.
[5]
PubMed ID11825893
JournalJ Biol Chem
Year2002
Volume277
Pages12868-73
AuthorsYang W, Rogers PA, Ding H
TitleRepair of nitric oxide-modified ferredoxin [2Fe-2S] cluster by cysteine desulfurase (IscS).
[6]
PubMed ID11972033
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages5948-52
AuthorsKato S, Mihara H, Kurihara T, Takahashi Y, Tokumoto U, Yoshimura T, Esaki N
TitleCys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: implications for the mechanism of iron-sulfur cluster assembly.
[7]
PubMed ID12382038
JournalAppl Microbiol Biotechnol
Year2002
Volume60
Pages12-23
AuthorsMihara H, Esaki N
TitleBacterial cysteine desulfurases: their function and mechanisms.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), PYRIDOXAL PHOSPHATE AT LYS-206, SUBUNIT, ACTIVE SITE CYS-328.
PubMed ID12860127
JournalJ Mol Biol
Year2003
Volume330
Pages1049-59
AuthorsCupp-Vickery JR, Urbina H, Vickery LE
TitleCrystal structure of IscS, a cysteine desulfurase from Escherichia coli.
Related PDB1p3w
[9]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), PYRIDOXAL PHOSPHATE AT LYS-231, ACTIVE SITE CYS-372.
PubMed ID15379559
JournalBiochemistry
Year2004
Volume43
Pages12210-9
AuthorsTirupati B, Vey JL, Drennan CL, Bollinger JM Jr
TitleKinetic and structural characterization of Slr0077/SufS, the essential cysteine desulfurase from Synechocystis sp. PCC 6803.
Related PDB1t3i
[10]
PubMed ID19883076
JournalBiochemistry
Year2009
Volume48
Pages12014-23
AuthorsBehshad E, Bollinger JM Jr
TitleKinetic analysis of cysteine desulfurase CD0387 from Synechocystis sp. PCC 6803: formation of the persulfide intermediate.
[11]
PubMed ID19308466
JournalJ Biol Inorg Chem
Year2009
Volume14
Pages829-39
AuthorsNuth M, Cowan JA
TitleIron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site.
[12]
PubMed ID19946146
JournalJ Biol Chem
Year2010
Volume285
Pages2302-8
AuthorsZhang W, Urban A, Mihara H, Leimkuhler S, Kurihara T, Esaki N
TitleIscS functions as a primary sulfur-donating enzyme by interacting specifically with MoeB and MoaD in the biosynthesis of molybdopterin in Escherichia coli.
[13]
PubMed ID20404999
JournalPLoS Biol
Year2010
Volume8
Pagese1000354
AuthorsShi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte A, Armengod ME, Cygler M
TitleStructural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
Related PDB3lvj,3lvk,3lvl,3lvm

comments
This enzyme catalyzes the elimination of sulfur from L-cysteine to produce L-alanine and sulfane sulfur, via a labile enzyme cysteinyl persulfide intermediate, utilizing pyridoxal 5'-phosphate (PLP). The persulfide sulfur is subsequently transferred to other proteins, such as iron-sulfur containing proteins, proteins related to sulfur-containing cofactor (thiamine, molybdopterin, biotin and lipoic acid) (see [7], [11], [12] and [13]).
This enzyme catalyzes the following reactions (see [3], [10]):
(A) Formation of external aldimine of PLP with amine group of L-cysteine (I00165) (from the internal aldimine with Lys).
(B) Isomerization of the Cys external aldimine to form a Cys ketimine intermediate(I00167), via a Cys quinonoid transition state (I00166).
(C) Transfer of thiol group from the ketimine intermediate (I00167) to active-site Cys, forming a persulfide intermediate (C15812) and an aminoacrylate intermediate (I00171).
(D) Isomerization of the aminoacrylate intermediate (I00171), to form an Ala ketimine intermediate (I00030).
(E) Isomerization of the Ala ketimine intermediate(I00030) to form an Ala external aldimine(I00049), via an Ala quinonoid transition state (I00032).
(F) Formation of internal aldimine of PLP with active-site Lys (from the external aldimine (I00049), releasing L-Ala from PLP.
(G) Transfer of thiol group from the persulfide intermediate (C15812) to the acceptor protein.
####
Acording to the literature [3] and [8], the catalytic residues play the following roles:
Asp205 and Gln208 (of 1t3i) may modulate the activity of PLP.
His128 might act as a general acid/base to protonate either PLP or Cys ketimine intermediate, deprotonate the thiol group of the active-site Cys, and protonate the aminoacrylate intermediate (I00171).
Lys231 may also act as a general acid/base to deprotonate and protonate the external aldimine intermediates (I00165 and I00049).
Cys372 acts as a nucleophile to accept the thiol group from the Cys ketimine intermediate(I00167), and transfers it to the acceptor protein.

createdupdated
2013-07-242013-11-14


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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