Escherichia coli K-12 substr. MG1655 Protein: Fe-S transport protein in Fe-S cluster assembly

Gene: sufA Accession Numbers: EG11378 (EcoCyc), b1684, ECK1680

Synonyms: ydiC

Regulation Summary Diagram: ?

Regulation summary diagram for sufA

Subunit composition of Fe-S transport protein in Fe-S cluster assembly = [SufA]2
         Fe-S cluster assembly, scaffold protein = SufA

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. SufA is the type II A-type carrier (ATC-II) [Vinella09] component of the Suf system for iron-sulfur cluster assembly that is utilized under iron starvation or oxidative stress conditions [Outten04]. SufA accepts Fe-S clusters formed by the SufBCD complex [Chahal09]; it was shown to carry a [2Fe-2S] cluster and to be able to transfer its cluster to target apoproteins such as ferredoxin (a [2Fe-2S]-containing protein) and aconitase A (a [4Fe-4S]-containing protein) [Gupta09].

Contradictory results of earlier studies - some of which are reported below - were likely due to purification of apo-SufA and in vitro assays under conditions that may not have been physiologically relevant [Gupta09].

SufA can accept sulfur atoms from the SufE component of the SufE-SufS cysteine desulfurase [Sendra07]; however, label transfer experiments don't show interactions between SufA and SufE/S [Chahal09]. In vitro, purified apoSufA can chelate iron-sulfur clusters by treatment with iron and sulfide under anaerobic conditions. HoloSufA then can form a fast and tight association with the target apoprotein biotin synthase (BioB) and transfers a [4Fe-4S] cluster to BioB in a slow reaction [OllagnierdeChou04]. Reports disagree on whether [Lu08] or not [Sendra07] purified apoSufA binds iron.

A crystal structure of SufA has been solved at 2.7 Å resolution. SufA forms a homodimer in the crystal structure, and the arrangement of four cysteine residues at the dimer interface may allow the coordination of an Fe-S cluster or an iron atom [Wada05].

The sufABCDSE operon encodes components of a secondary pathway of iron-sulfur cluster assembly; the isc operon encodes the major assembly pathway [Takahashi02]. A sufABCDSE operon deletion mutation leads to increased sensitivity to superoxide-generating agents [Lee04], whereas a sufABCDSE isc double mutant exhibits synthetic lethality, indicating that these systems are redundant and that iron-sulfur cluster assembly is essential for viability [Takahashi02, Tokumoto04]. A sufA iscA double mutant has a severe growth defect under aerobic conditions in minimal or rich medium [Lu08, Vinella09] due to the lack of 4Fe-4S clusters in metabolically essential enzymes such as IlvD, ThiC [Tan09], and IspG/H [Vinella09]. A sufA iscA double mutant is viable under anaerobic conditions [Vinella09].

Overproduction of the products of the sufABCDSE operon, or regulatory mutations in the sufABCDSE operon, suppress defects of a strain deleted of the isc operon [Takahashi02]. Cobalt inhibits growth of E. coli due to a toxic effect on metabolically essential Fe-S cluster-containing proteins. suf mutant strains are hypersensitive to cobalt; thus, the Suf system may be involved in Fe-S cluster repair [Ranquet07].

Expression of sufA is induced by superoxide generators and hydrogen peroxide [Lee04]. Regulation occurs via the iron-dependent Fur repressor [Patzer99], OxyR, IHF, and IscR [Lee04, Yeo06, Lee08a].

Reviews: [Johnson05, Fontecave05, Barras05]

Gene Citations: [Zheng01a]

Locations: cytosol

Map Position: [1,762,042 <- 1,762,410] (37.98 centisomes, 137°)
Length: 369 bp / 122 aa

Molecular Weight of Polypeptide: 13.3 kD (from nucleotide sequence)

Molecular Weight of Multimer: 30.2 kD (experimental) [Gupta09]

Unification Links: ASAP:ABE-0005624 , EchoBASE:EB1352 , EcoGene:EG11378 , EcoliWiki:b1684 , ModBase:P77667 , OU-Microarray:b1684 , PortEco:sufA , PR:PRO_000024006 , Pride:P77667 , Protein Model Portal:P77667 , RefSeq:NP_416199 , RegulonDB:EG11378 , SMR:P77667 , String:511145.b1684 , UniProt:P77667

Relationship Links: InterPro:IN-FAMILY:IPR000361 , InterPro:IN-FAMILY:IPR011298 , InterPro:IN-FAMILY:IPR016092 , InterPro:IN-FAMILY:IPR017870 , PDB:Structure:2D2A , 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 sufA

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Lee04]
GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA01a, Vinella09]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Chahal09]
GO:0042803 - protein homodimerization activity Inferred from experiment [Gupta09]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment [Gupta09]
GO:0005198 - structural molecule activity Inferred by computational analysis [GOA01a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism incorporation of metal ions
metabolism metabolism of other compounds sulfur metabolism

Essentiality data for sufA 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 14-Oct-2009 by Keseler I , SRI International
Last-Curated ? 15-Oct-2009 by Keseler I , SRI International

Sequence Features

Protein sequence of Fe-S cluster assembly, scaffold protein with features indicated

Feature Class Location Common Name Citations
Amino-Acid-Sites-That-Bind 50, 114, 116 sulfur binding residues

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


1/26/1998 (pkarp) Merged genes G6910/b1684 and EG11378/ydiC


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

Chahal09: Chahal HK, Dai Y, Saini A, Ayala-Castro C, Outten FW (2009). "The SufBCD Fe-S scaffold complex interacts with SufA for Fe-S cluster transfer." Biochemistry 48(44);10644-53. PMID: 19810706

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

Fontecave05: Fontecave M, Choudens SO, Py B, Barras F (2005). "Mechanisms of iron-sulfur cluster assembly: the SUF machinery." J Biol Inorg Chem 10(7);713-21. PMID: 16211402

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

Gupta09: Gupta V, Sendra M, Naik SG, Chahal HK, Huynh BH, Outten FW, Fontecave M, Ollagnier de Choudens S (2009). "Native Escherichia coli SufA, coexpressed with SufBCDSE, purifies as a [2Fe-2S] protein and acts as an Fe-S transporter to Fe-S target enzymes." J Am Chem Soc 131(17);6149-53. PMID: 19366265

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

Lee04: Lee JH, Yeo WS, Roe JH (2004). "Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor." Mol Microbiol 51(6);1745-55. PMID: 15009899

Lee08a: Lee KC, Yeo WS, Roe JH (2008). "Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through Fur and IscR in Escherichia coli." J Bacteriol 190(24);8244-7. PMID: 18849427

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

OllagnierdeChou04: Ollagnier-de-Choudens S, Sanakis Y, Fontecave M (2004). "SufA/IscA: reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly." J Biol Inorg Chem 9(7);828-38. PMID: 15278785

Outten04: Outten FW, Djaman O, Storz G (2004). "A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli." Mol Microbiol 52(3);861-72. PMID: 15101990

Patzer99: Patzer SI, Hantke K (1999). "SufS is a NifS-like protein, and SufD is necessary for stability of the [2Fe-2S] FhuF protein in Escherichia coli." J Bacteriol 181(10);3307-9. PMID: 10322040

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

Sendra07: Sendra M, Ollagnier de Choudens S, Lascoux D, Sanakis Y, Fontecave M (2007). "The SUF iron-sulfur cluster biosynthetic machinery: sulfur transfer from the SUFS-SUFE complex to SUFA." FEBS Lett 581(7);1362-8. PMID: 17350000

Takahashi02: Takahashi Y, Tokumoto U (2002). "A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids." J Biol Chem 277(32);28380-3. PMID: 12089140

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

Tokumoto04: Tokumoto U, Kitamura S, Fukuyama K, Takahashi Y (2004). "Interchangeability and distinct properties of bacterial Fe-S cluster assembly systems: functional replacement of the isc and suf operons in Escherichia coli with the nifSU-like operon from Helicobacter pylori." J Biochem (Tokyo) 136(2);199-209. PMID: 15496591

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

Wada05: Wada K, Hasegawa Y, Gong Z, Minami Y, Fukuyama K, Takahashi Y (2005). "Crystal structure of Escherichia coli SufA involved in biosynthesis of iron-sulfur clusters: implications for a functional dimer." FEBS Lett 579(29);6543-8. PMID: 16298366

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

Zheng01a: 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

Other References Related to Gene Regulation

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

Jang10: Jang S, Imlay JA (2010). "Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate." Mol Microbiol 78(6);1448-67. PMID: 21143317

Mettert14: Mettert EL, Kiley PJ (2014). "Coordinate regulation of the Suf and Isc Fe-S cluster biogenesis pathways by IscR is essential for viability of Escherichia coli." J Bacteriol 196(24);4315-23. PMID: 25266384

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

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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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