Escherichia coli K-12 substr. MG1655 Protein: iron-sulfur cluster assembly protein

Gene: iscA Accession Numbers: EG12132 (EcoCyc), b2528, ECK2525

Synonyms: yfhF

Regulation Summary Diagram: ?

Regulation summary diagram for iscA

Subunit composition of iron-sulfur cluster assembly protein = [IscA]4
         iron-sulfur cluster assembly protein = IscA

The assembly of iron-sulfur clusters requires complex biosynthetic machinery. E. coli encodes two sets of proteins, the Isc and the Suf system, to achieve this task. IscA is the type II A-type carrier (ATC-II) of the Isc system [Vinella09]. IscA acts as an iron chaperone [Yang06]. In the presence of the thioreductase system, IscA has been shown to bind iron with an association constant of 2x1019 M-1 [Ding05]. In vitro in the presence of IscS and L-cysteine, IscA can provide iron to the scaffold protein IscU [Ding04b, Ding05a, Yang06], and IscA mutants unable to bind iron are unable to perform this function [Ding04a]. IscA was shown to bind iron in vivo [Wang10a].

In the presence of hydrogen peroxide, IscA loses its iron binding activity due to oxidation of its thiol groups [Ding07]. IscA can utilize iron bound by FtnA [Bitoun08].

Crystal structures of IscA are presented at 2.3 Å resolution. IscA forms a dimer of dimers [Bilder04, CuppVickery04].

IscA and HscA physically interact [Tokumoto02]. The [2Fe-2S] cluster-bound form of IscA interacts with ferredoxin, resulting in transfer of the [2Fe-2S] cluster to form holoferredoxin [OllagnierdeChou01, Bonomi05]. Under physiologically relevant conditions, IscA iacts as an iron chaperone rather than an iron-sulfur cluster assembly scaffold protein [Yang06].

Mutagenesis of the conserved C99 or C101 residues abolishes the iron binding and transfer activities of IscA [Ding04a]. Overexpression of a gene cluster containing the iscA region results in increased formation of iron-sulfur clusters in various overexpressed ferredoxins [Nakamura99]. Conversely, an iscA mutation limits iron-sulfur cluster assembly in overexpressed ferredoxin [Takahashi99]. An iscA insertion mutant does not have a significant growth defect [Tokumoto01], but an iscA sufA double mutant has a severe growth defect under aerobic conditions in minimal or rich medium [Lu08, Vinella09] due to lack of [4Fe-4S] clusters in metabolically essential enzymes such as IlvD, ThiC [Tan09], and IspG/H [Vinella09]. The double mutant can be rescued by addition of either IscA or SufA, indicating that IscA and SufA provide redundant functions aerobically [Lu08]. Under anaerobic conditions, an iscA sufA double mutant is viable, while an iscA erpA double mutant is lethal unless mevalonate is provided in the medium [Vinella09]. In an iscA null mutant, activity of Fdh-N, Fdh-O, and nitrate reductase is strongly reduced [Pinske12] and neither hydrogenase 1 nor hydrogenase 2 activity is detectable [Pinske12a] due to the absence of the [Fe-S] cluster-containing small subunits of these enzymes.

IscA: "iron-sulfur cluster

Reviews: [Barras05, Johnson05, Fontecave08, Py10]

Gene Citations: [Schwartz01]

Locations: cytosol

Map Position: [2,657,585 <- 2,657,908] (57.28 centisomes, 206°)
Length: 324 bp / 107 aa

Molecular Weight of Polypeptide: 11.556 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008319 , DIP:DIP-35854N , EchoBASE:EB2053 , EcoGene:EG12132 , EcoliWiki:b2528 , ModBase:P0AAC8 , OU-Microarray:b2528 , PortEco:iscA , PR:PRO_000023031 , Pride:P0AAC8 , Protein Model Portal:P0AAC8 , RefSeq:NP_417023 , RegulonDB:EG12132 , SMR:P0AAC8 , String:511145.b2528 , UniProt:P0AAC8

Relationship Links: InterPro:IN-FAMILY:IPR000361 , InterPro:IN-FAMILY:IPR011302 , InterPro:IN-FAMILY:IPR016092 , InterPro:IN-FAMILY:IPR017870 , PDB:Structure:1R94 , PDB:Structure:1R95 , PDB:Structure:1S98 , Pfam:IN-FAMILY:PF01521 , Prosite:IN-FAMILY:PS01152

In Paralogous Gene Group: 55 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for iscA

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Takahashi99, OllagnierdeChou01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, OllagnierdeChou01, Tokumoto02]
GO:0008198 - ferrous iron binding Inferred from experiment [Ding04b]
GO:0034986 - iron chaperone activity Inferred from experiment [Ding04a, Ding04b]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment [OllagnierdeChou01]
GO:0005198 - structural molecule activity Inferred by computational analysis [GOA01a]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA06, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer protein related chaperoning, repair (refolding)
metabolism central intermediary metabolism incorporation of metal ions

Essentiality data for iscA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Created 20-Oct-2010 by Keseler I , SRI International
Last-Curated ? 30-Mar-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of iron-sulfur cluster assembly protein with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 35
[Ding04a, UniProt11]
UniProt: Decrease of iron binding activity.
Metal-Binding-Site 35
UniProt: Iron; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 99
[Ding04a, UniProt11]
UniProt: Loss of iron binding activity.
Metal-Binding-Site 99
UniProt: Iron; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 101
[Ding04a, UniProt11]
UniProt: Loss of iron binding activity.
Metal-Binding-Site 101
UniProt: Iron; Non-Experimental Qualifier: probable;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2528 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12132; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Barras05: Barras F, Loiseau L, Py B (2005). "How Escherichia coli and Saccharomyces cerevisiae build Fe/S proteins." Adv Microb Physiol 50;41-101. PMID: 16221578

Bilder04: Bilder PW, Ding H, Newcomer ME (2004). "Crystal structure of the ancient, Fe-S scaffold IscA reveals a novel protein fold." Biochemistry 43(1);133-9. PMID: 14705938

Bitoun08: Bitoun JP, Wu G, Ding H (2008). "Escherichia coli FtnA acts as an iron buffer for re-assembly of iron-sulfur clusters in response to hydrogen peroxide stress." Biometals 21(6);693-703. PMID: 18618270

Bonomi05: Bonomi F, Iametti S, Ta D, Vickery LE (2005). "Multiple turnover transfer of [2Fe2S] clusters by the iron-sulfur cluster assembly scaffold proteins IscU and IscA." J Biol Chem 280(33);29513-8. PMID: 15964837

CuppVickery04: Cupp-Vickery JR, Silberg JJ, Ta DT, Vickery LE (2004). "Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli." J Mol Biol 338(1);127-37. PMID: 15050828

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Ding04a: Ding H, Clark RJ, Ding B (2004). "IscA mediates iron delivery for assembly of iron-sulfur clusters in IscU under the limited accessible free iron conditions." J Biol Chem 279(36);37499-504. PMID: 15247288

Ding04b: Ding H, Clark RJ (2004). "Characterization of iron binding in IscA, an ancient iron-sulphur cluster assembly protein." Biochem J 379(Pt 2);433-40. PMID: 14720122

Ding05: Ding H, Harrison K, Lu J (2005). "Thioredoxin reductase system mediates iron binding in IscA and iron delivery for the iron-sulfur cluster assembly in IscU." J Biol Chem 280(34);30432-7. PMID: 15985427

Ding05a: Ding B, Smith ES, Ding H (2005). "Mobilization of the iron centre in IscA for the iron-sulphur cluster assembly in IscU." Biochem J 389(Pt 3);797-802. PMID: 15828873

Ding07: Ding H, Yang J, Coleman LC, Yeung S (2007). "Distinct iron binding property of two putative iron donors for the iron-sulfur cluster assembly: IscA and the bacterial frataxin ortholog CyaY under physiological and oxidative stress conditions." J Biol Chem 282(11);7997-8004. PMID: 17244611

Fontecave08: Fontecave M, Ollagnier-de-Choudens S (2008). "Iron-sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer." Arch Biochem Biophys 474(2);226-37. PMID: 18191630

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Johnson05: Johnson DC, Dean DR, Smith AD, Johnson MK (2005). "Structure, function, and formation of biological iron-sulfur clusters." Annu Rev Biochem 74;247-81. PMID: 15952888

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lu08: Lu J, Yang J, Tan G, Ding H (2008). "Complementary roles of SufA and IscA in the biogenesis of iron-sulfur clusters in Escherichia coli." Biochem J 409(2);535-43. PMID: 17941825

Nakamura99: Nakamura M, Saeki K, Takahashi Y (1999). "Hyperproduction of recombinant ferredoxins in escherichia coli by coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hs cA-fdx-ORF3 gene cluster." J Biochem (Tokyo) 126(1);10-8. PMID: 10393315

OllagnierdeChou01: Ollagnier-de-Choudens S, Mattioli T, Takahashi Y, Fontecave M (2001). "Iron-sulfur cluster assembly: characterization of IscA and evidence for a specific and functional complex with ferredoxin." J Biol Chem 276(25);22604-7. PMID: 11319236

Pinske12: Pinske C, Sawers RG (2012). "A-type carrier protein ErpA is essential for formation of an active formate-nitrate respiratory pathway in Escherichia coli K-12." J Bacteriol 194(2);346-53. PMID: 22081393

Pinske12a: Pinske C, Sawers RG (2012). "Delivery of Iron-Sulfur Clusters to the Hydrogen-Oxidizing [NiFe]-Hydrogenases in Escherichia coli Requires the A-Type Carrier Proteins ErpA and IscA." PLoS One 7(2);e31755. PMID: 22363723

Py10: Py B, Barras F (2010). "Building Fe-S proteins: bacterial strategies." Nat Rev Microbiol 8(6);436-46. PMID: 20467446

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Schwartz01: Schwartz CJ, Giel JL, Patschkowski T, Luther C, Ruzicka FJ, Beinert H, Kiley PJ (2001). "IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins." Proc Natl Acad Sci U S A 2001;98(26);14895-900. PMID: 11742080

Takahashi99: Takahashi Y, Nakamura M (1999). "Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli." J Biochem (Tokyo) 1999;126(5);917-26. PMID: 10544286

Tan09: Tan G, Lu J, Bitoun JP, Huang H, Ding H (2009). "IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways in Escherichia coli under aerobic growth conditions." Biochem J 420(3);463-72. PMID: 19309314

Tokumoto01: Tokumoto U, Takahashi Y (2001). "Genetic analysis of the isc operon in Escherichia coli involved in the biogenesis of cellular iron-sulfur proteins." J Biochem (Tokyo) 130(1);63-71. PMID: 11432781

Tokumoto02: Tokumoto U, Nomura S, Minami Y, Mihara H, Kato S, Kurihara T, Esaki N, Kanazawa H, Matsubara H, Takahashi Y (2002). "Network of protein-protein interactions among iron-sulfur cluster assembly proteins in Escherichia coli." J Biochem (Tokyo) 131(5);713-9. PMID: 11983079

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vinella09: Vinella D, Brochier-Armanet C, Loiseau L, Talla E, Barras F (2009). "Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers." PLoS Genet 5(5);e1000497. PMID: 19478995

Wang10a: Wang W, Huang H, Tan G, Si F, Liu M, Landry AP, Lu J, Ding H (2010). "In vivo evidence for the iron-binding activity of an iron-sulfur cluster assembly protein IscA in Escherichia coli." Biochem J 432(3);429-36. PMID: 20942799

Yang06: Yang J, Bitoun JP, Ding H (2006). "Interplay of IscA and IscU in biogenesis of iron-sulfur clusters." J Biol Chem 281(38);27956-63. PMID: 16877383

Other References Related to Gene Regulation

Desnoyers09: Desnoyers G, Morissette A, Prevost K, Masse E (2009). "Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA." EMBO J 28(11);1551-61. PMID: 19407815

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

Giel13: Giel JL, Nesbit AD, Mettert EL, Fleischhacker AS, Wanta BT, Kiley PJ (2013). "Regulation of iron-sulphur cluster homeostasis through transcriptional control of the Isc pathway by [2Fe-2S]-IscR in Escherichia coli." Mol Microbiol 87(3);478-92. PMID: 23075318

Mihara08: Mihara H, Hidese R, Yamane M, Kurihara T, Esaki N (2008). "The iscS gene deficiency affects the expression of pyrimidine metabolism genes." Biochem Biophys Res Commun 372(3);407-11. PMID: 18482579

Prevost11: Prevost K, Desnoyers G, Jacques JF, Lavoie F, Masse E (2011). "Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage." Genes Dev 25(4);385-96. PMID: 21289064

Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183

Yeo06: Yeo WS, Lee JH, Lee KC, Roe JH (2006). "IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins." Mol Microbiol 61(1);206-18. PMID: 16824106

Zheng01: Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G (2001). "DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide." J Bacteriol 183(15);4562-70. PMID: 11443091

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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