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Escherichia coli K-12 substr. MG1655 Polypeptide: scaffold protein for iron-sulfur cluster assembly



Gene: iscU Accession Numbers: G7324 (EcoCyc), b2529, ECK2526

Synonyms: yfhN, nifU

Regulation Summary Diagram: ?

Summary:
IscU is the scaffold protein for assembly and transfer of iron-sulfur clusters. The cysteine desulfurase IscS transfers the sulfane sulfur to IscU, IscA acts as the iron chaperone, CyaY appears to regulate cluster assembly, and the HscA and HscB chaperone and cochaperone facilitate Fe-S cluster transfer.

IscU is able to form [2Fe-2S] clusters and transfer them to apo-ferredoxin, acting catalytically [Bonomi05, Bonomi08]. The chaperones HscA and HscB and ATP hydrolysis by HscA accelerate cluster transfer [Bonomi08].

The C terminus of IscS interacts with IscU and transfers sulfur directly to IscU [Urbina01, Kato02, Kurihara03]. The mechanism of transfer is discussed [Kato02, Kurihara03]. In the presence of IscS, IscU is able to form [2Fe-2S] clusters that are converted to [4Fe-4S] clusters; CyaY appears to slow this process [Iannuzzi11]. In the presence of IscS and L-cysteine, the IscA protein is able to deliver iron to IscU [Ding04, Ding04a, Ding05, Ding05a, Yang06]; purified IscU does not bind iron directly [Adinolfi04, Wang10]. Cobalt is toxic to the cell, which may be due to its ability to replace iron in the Fe-S cluster of IscU [Ranquet07].

Although CyaY can function as an iron donor to IscU in the presence of IscS and cysteine [Layer06], it was later shown that it inhibits Fe-S cluster formation on IscU [Adinolfi09] by slowing the reaction [Iannuzzi11].

HscA exhibits chaperone activity toward IscU, and this activity is suggested to play a role in iron-sulfur cluster maturation [Silberg01]. IscU binds to both HscB and HscA [Hoff00, Tokumoto02, Hoff02, Hoff03, Tapley04], interacting with both the ATP- and ADP-bound HscA; together with the co-chaperone HscB, it stimulates the ATPase activity of HscA [Hoff00, Silberg04]. IscU interacts with the C-terminal domain of HscB [Fuzery11]. Site-directed mutagenesis of potential Fe-S cluster ligands in IscU suggests specific roles for individual cysteine residues; a model for chaperone-facilitated cluster transfer has been proposed [Bonomi11].

IscU has been reported to be either dimeric [Kato02] or monomeric [Adinolfi04] in solution. The 24.3 kDa molecular weight obtained by analytical gel filtration may result from the partly unstructured nature of the protein [Fuzery08]. Solution structures shows that apo-IscU exists in two different conformations, one disordered, and another largely ordered, which interconvert quickly [Kim09, Kim12]. IscS preferentially interacts with and stabilizes the disordered state of IscU, and mutants that stabilize the ordered state of IscU show significantly slower cluster assembly than wild type [Kim12]. HscB binds to and stabilizes the ordered state of IscU; the surface region of IscU which interacts with HscB has been identified [Kim09].

The interaction between IscU and IscS has been studied by NMR [Prischi10]. A co-crystal structure of the IscS-IscU complex from E. coli O157:H7 EDL933 has been reported [Shi10].

Co-overproduction of IscU with eight polypeptides produced from neighboring genes (trmJ-iscR-iscS-iscU-iscA-hscB-hscA-fdx-iscX) causes increased ferredoxin iron-sulfur cluster assembly [Nakamura99]. An iscU mutant has a growth defect compared to wild type [Tokumoto01, Djaman04]. It has very low activity of the iron-sulfur cluster enzymes succinate dehydrogenase and glutamate synthase [Tokumoto01] and no formate dehydrogenase, nitrate reductase [Pinske12], hydrogenase 1 and hydrogenase 2 activity [Pinske12a]. An iscU mutant also contains no HypD, the Fe-S cluster-containing hydrogenase maturase [Pinske12a].

Transcription of the isc operon is repressed by the IscR protein, which contains an iron-sulfur cluster that could act as a sensor of iron-sulfur cluster assembly and regulate expression of the isc operon accordingly [Schwartz01].

IscU: "iron-sulfur-cluster formation" [Zheng98]

Reviews: [Frazzon02, Johnson05, AyalaCastro08, Bandyopadhyay08, Py10]

Citations: [Wu12]

Gene Citations: [Takahashi99]

Locations: cytosol

Map Position: [2,657,925 <- 2,658,311] (57.29 centisomes)
Length: 387 bp / 128 aa

Molecular Weight of Polypeptide: 13.849 kD (from nucleotide sequence), 17.0 kD (experimental) [Hoff00 ]

Unification Links: ASAP:ABE-0008321 , DIP:DIP-48025N , EchoBASE:EB3176 , EcoGene:EG13395 , EcoliWiki:b2529 , ModBase:P0ACD4 , OU-Microarray:b2529 , PortEco:iscU , PR:PRO_000023383 , Pride:P0ACD4 , Protein Model Portal:P0ACD4 , RefSeq:NP_417024 , RegulonDB:G7324 , SMR:P0ACD4 , String:511145.b2529 , Swiss-Model:P0ACD4 , UniProt:P0ACD4

Relationship Links: InterPro:IN-FAMILY:IPR002871 , InterPro:IN-FAMILY:IPR011339 , PDB:Structure:2KQK , PDB:Structure:2L4X , Pfam:IN-FAMILY:PF01592

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA01, Bonomi05]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05, Arifuzzaman06, Urbina01, Hoff00, Kato02]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Kato02]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment [Adinolfi04]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment [Iannuzzi11]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer protein related posttranslational modification
metabolism biosynthesis of building blocks cofactors, small molecule carriers
metabolism metabolism of other compounds sulfur metabolism

Essentiality data for iscU 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]

Credits:
Last-Curated ? 22-Mar-2012 by Keseler I , SRI International


Sequence Features

Feature Class Location Common Name Citations
Cleavage-of-Initial-Methionine 1  
[Hoff00]
Protein-Binding-Region 99 -> 103 interacts with HscA
[Hoff02, Hoff03]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Adinolfi04: Adinolfi S, Rizzo F, Masino L, Nair M, Martin SR, Pastore A, Temussi PA (2004). "Bacterial IscU is a well folded and functional single domain protein." Eur J Biochem 271(11);2093-100. PMID: 15153099

Adinolfi09: Adinolfi S, Iannuzzi C, Prischi F, Pastore C, Iametti S, Martin SR, Bonomi F, Pastore A (2009). "Bacterial frataxin CyaY is the gatekeeper of iron-sulfur cluster formation catalyzed by IscS." Nat Struct Mol Biol 16(4);390-6. PMID: 19305405

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

AyalaCastro08: Ayala-Castro C, Saini A, Outten FW (2008). "Fe-S cluster assembly pathways in bacteria." Microbiol Mol Biol Rev 72(1);110-25, table of contents. PMID: 18322036

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

Bandyopadhyay08: Bandyopadhyay S, Chandramouli K, Johnson MK (2008). "Iron-sulfur cluster biosynthesis." Biochem Soc Trans 36(Pt 6);1112-9. PMID: 19021507

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

Bonomi08: Bonomi F, Iametti S, Morleo A, Ta D, Vickery LE (2008). "Studies on the mechanism of catalysis of iron-sulfur cluster transfer from IscU[2Fe2S] by HscA/HscB chaperones." Biochemistry 47(48);12795-801. PMID: 18986169

Bonomi11: Bonomi F, Iametti S, Morleo A, Ta D, Vickery LE (2011). "Facilitated transfer of IscU-[2Fe2S] clusters by chaperone-mediated ligand exchange." Biochemistry 50(44);9641-50. PMID: 21977977

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Ding04: 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

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

Ding05: 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

Ding05a: 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

Djaman04: Djaman O, Outten FW, Imlay JA (2004). "Repair of oxidized iron-sulfur clusters in Escherichia coli." J Biol Chem 279(43):44590-9. PMID: 15308657

Frazzon02: Frazzon J, Fick JR, Dean DR (2002). "Biosynthesis of iron-sulphur clusters is a complex and highly conserved process." Biochem Soc Trans 30(4);680-5. PMID: 12196163

Fuzery08: Fuzery AK, Tonelli M, Ta DT, Cornilescu G, Vickery LE, Markley JL (2008). "Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU." Biochemistry 47(36);9394-404. PMID: 18702525

Fuzery11: Fuzery AK, Oh JJ, Ta DT, Vickery LE, Markley JL (2011). "Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex." BMC Biochem 12;3. PMID: 21269500

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hoff00: Hoff KG, Silberg JJ, Vickery LE (2000). "Interaction of the iron-sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system of Escherichia coli." Proc Natl Acad Sci U S A 97(14);7790-5. PMID: 10869428

Hoff02: Hoff KG, Ta DT, Tapley TL, Silberg JJ, Vickery LE (2002). "Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU." J Biol Chem 277(30);27353-9. PMID: 11994302

Hoff03: Hoff KG, Cupp-Vickery JR, Vickery LE (2003). "Contributions of the LPPVK motif of the iron-sulfur template protein IscU to interactions with the Hsc66-Hsc20 chaperone system." J Biol Chem 278(39):37582-9. PMID: 12871959

Iannuzzi11: Iannuzzi C, Adinolfi S, Howes BD, Garcia-Serres R, Clemancey M, Latour JM, Smulevich G, Pastore A (2011). "The role of CyaY in iron sulfur cluster assembly on the E. coli IscU scaffold protein." PLoS One 6(7);e21992. PMID: 21799759

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

Kato02: Kato S, Mihara H, Kurihara T, Takahashi Y, Tokumoto U, Yoshimura T, Esaki N (2002). "Cys-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." Proc Natl Acad Sci U S A 99(9);5948-52. PMID: 11972033

Kim09: Kim JH, Fuzery AK, Tonelli M, Ta DT, Westler WM, Vickery LE, Markley JL (2009). "Structure and dynamics of the iron-sulfur cluster assembly scaffold protein IscU and its interaction with the cochaperone HscB." Biochemistry 48(26);6062-71. PMID: 19492851

Kim12: Kim JH, Tonelli M, Markley JL (2012). "Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase." Proc Natl Acad Sci U S A 109(2);454-9. PMID: 22203963

Kurihara03: Kurihara T, Mihara H, Kato S, Yoshimura T, Esaki N (2003). "Assembly of iron-sulfur clusters mediated by cysteine desulfurases, IscS, CsdB and CSD, from Escherichia coli." Biochim Biophys Acta 1647(1-2);303-9. PMID: 12686149

Layer06: Layer G, Ollagnier-de Choudens S, Sanakis Y, Fontecave M (2006). "Iron-sulfur cluster biosynthesis: characterization of Escherichia coli CYaY as an iron donor for the assembly of [2Fe-2S] clusters in the scaffold IscU." J Biol Chem 281(24);16256-63. PMID: 16603772

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

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

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

Prischi10: Prischi F, Pastore C, Carroni M, Iannuzzi C, Adinolfi S, Temussi P, Pastore A (2010). "Of the vulnerability of orphan complex proteins: the case study of the E. coli IscU and IscS proteins." Protein Expr Purif 73(2);161-6. PMID: 20471481

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

Ranquet07: Ranquet C, Ollagnier-de-Choudens S, Loiseau L, Barras F, Fontecave M (2007). "Cobalt stress in Escherichia coli. The effect on the iron-sulfur proteins." J Biol Chem 282(42);30442-51. PMID: 17642475

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

Shi10: Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte A, Armengod ME, Cygler M (2010). "Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions." PLoS Biol 8(4);e1000354. PMID: 20404999

Silberg01: Silberg JJ, Hoff KG, Tapley TL, Vickery LE (2001). "The Fe/S assembly protein IscU behaves as a substrate for the molecular chaperone Hsc66 from Escherichia coli." J Biol Chem 276(3);1696-700. PMID: 11053447

Silberg04: Silberg JJ, Tapley TL, Hoff KG, Vickery LE (2004). "Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU." J Biol Chem 279(52):53924-31. PMID: 15485839

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

Tapley04: Tapley TL, Vickery LE (2004). "Preferential substrate binding orientation by the molecular chaperone HscA." J Biol Chem 279(27);28435-42. PMID: 15100228

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

Urbina01: Urbina HD, Silberg JJ, Hoff KG, Vickery LE (2001). "Transfer of sulfur from IscS to IscU during Fe/S cluster assembly." J Biol Chem 276(48);44521-6. PMID: 11577100

Wang10: 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

Wu12: Wu G, Li L (2012). "Biochemical Characterization of Iron-Sulfur Cluster Assembly in the Scaffold IscU of Escherichia coli." Biochemistry (Mosc) 77(2);135-42. PMID: 22348472

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

Zheng98: Zheng L, Cash VL, Flint DH, Dean DR (1998). "Assembly of iron-sulfur clusters. Identification of an iscSUA-hscBA-fdx gene cluster from Azotobacter vinelandii." J Biol Chem 273(21);13264-72. PMID: 9582371

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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