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Escherichia coli K-12 substr. MG1655 Protein: SufBC2D Fe-S cluster scaffold complex

Subunit composition of SufBC2D Fe-S cluster scaffold complex = [SufB][SufC]2[SufD]
         SufB component of SufBCD Fe-S cluster scaffold complex = SufB (extended summary available)
         SufC component of SufBCD Fe-S cluster scaffold complex = SufC (extended summary available)
         SufD component of SufBCD Fe-S cluster scaffold complex = SufD (extended summary available)

Summary:
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. The SufBC2D complex functions as the scaffold for de novo assembly of Fe-S clusters [Chahal09]; it can perform assembly of a [4Fe-4S] cluster in vitro and transfer it to target proteins [Wollers10].

The SufBCD complex can be primarily isolated in a 1:2:1 stoichiometry of the SufB:SufC:SufD subunits; this complex can not be assembled in vitro from isolated components. When purified anaerobically, the complex contains 1 eq of FADH2; the complex does not bind the oxidized form, FAD [Wollers10].

Reviews: [Johnson05, Fontecave05, Barras05, Py10]

Molecular Weight: 156.6 kD (experimental) [Wollers10 ]

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment [Wollers10]
Molecular Function: GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment [Wollers10]
GO:0071950 - FADH2 binding Inferred from experiment [Wollers10]

Credits:
Last-Curated ? 01-Oct-2010 by Keseler I , SRI International


Subunit of SufBC2D Fe-S cluster scaffold complex: SufB component of SufBCD Fe-S cluster scaffold complex

Synonyms: YnhE, SufB

Gene: sufB Accession Numbers: G6909 (EcoCyc), b1683, ECK1679

Locations: cytosol

Sequence Length: 495 AAs

Molecular Weight: 54.745 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA01, Takahashi02]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Wollers10, Chahal09, Wada09, Butland05, Layer07]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment [Layer07]
Cellular Component: GO:0005737 - cytoplasm
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

Unification Links: DIP:DIP-10938N , EcoliWiki:b1683 , ModBase:P77522 , PR:PRO_000024007 , Pride:P77522 , Protein Model Portal:P77522 , RefSeq:NP_416198 , SMR:P77522 , String:511145.b1683 , UniProt:P77522

Relationship Links: InterPro:IN-FAMILY:IPR000825 , InterPro:IN-FAMILY:IPR010231 , Pfam:IN-FAMILY:PF01458

Summary:
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. The SufE protein transfers sulfur to SufB [Layer07], which is a component of the SufBC2D Fe-S cluster assembly scaffold complex. The SufBCD complex activates the cysteine desulfurase activity of SufSE, likely by acting as the sulfur acceptor [Outten03, Layer07].

SufB and SufC were reported to be associated with membranes by immuno-EM [Rangachari02], but studies conducted in Erwinia chrysanthemi indicate that the homologs are cytoplasmic [Loiseau03].

A sufABCDSE operon deletion mutation leads to increased sensitivity to superoxide-generating agents [Lee04a], 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]. 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].

Expression of sufA, the first gene in the sufABCDSE operon, is induced by superoxide generators and hydrogen peroxide [Lee04a]. Regulation occurs via the iron-dependent Fur repressor [Patzer99], OxyR, IHF, and IscR [Lee04a, Yeo06, Lee08].

Reviews: [Johnson05, Fontecave05, Barras05, Py10]

Essentiality data for sufB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of SufBC2D Fe-S cluster scaffold complex: SufC component of SufBCD Fe-S cluster scaffold complex

Synonyms: YnhD, SufC

Gene: sufC Accession Numbers: G6908 (EcoCyc), b1682, ECK1678

Locations: cytosol

Sequence Length: 248 AAs

Molecular Weight: 27.582 kD (from nucleotide sequence)

Molecular Weight: 27.6 kD (experimental) [Wollers10]

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment [Saini10]
GO:0006200 - ATP catabolic process Inferred by computational analysis [GOA01]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Wollers10, Layer07, Chahal09, Wada09, Butland05]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016887 - ATPase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

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

Unification Links: DIP:DIP-10939N , EcoliWiki:b1682 , Mint:MINT-7290829 , ModBase:P77499 , Pride:P77499 , Protein Model Portal:P77499 , RefSeq:NP_416197 , SMR:P77499 , String:511145.b1682 , Swiss-Model:P77499 , UniProt:P77499

Relationship Links: InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR010230 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2D3W , PDB:Structure:2ZU0 , Pfam:IN-FAMILY:PF00005 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893 , Smart:IN-FAMILY:SM00382

Summary:
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. SufC is a component of the SufBC2D Fe-S cluster assembly scaffold complex. The ATPase activity of SufC is required for iron acquisition in vivo, and both SufC and SufD are required for Fe-S cluster formation on SufB in vivo [Saini10].

A crystal structure of SufC has been determined at 2.5 Å resolution [Kitaoka06], and a crystal structure of the SufC2-SufD2 complex has been determined at 2.2 Å resolution [Wada09]. Upon associating with SufD, the structure of SufC changes to become competent for ATP binding and hydrolysis [Wada09].

SufB and SufC were reported to be associated with membranes by immuno-EM [Rangachari02], but studies conducted in Erwinia chrysanthemi indicate that the homologs are cytoplasmic [Loiseau03].

A sufABCDSE operon deletion mutation leads to increased sensitivity to superoxide-generating agents [Lee04a], 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]. 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]. A non-polar sufC mutant shows lower induction of soxS expression in response to paraquat, indicating a possible effect on the [2Fe-2S] cluster of SoxR [Nachin01].

Expression of sufA, the first gene in the sufABCDSE operon, is induced by superoxide generators and hydrogen peroxide [Lee04a]. Regulation occurs via the iron-dependent Fur repressor [Patzer99], OxyR, IHF, and IscR [Lee04a, Yeo06, Lee08].

Reviews: [Richardson03, Johnson05, Fontecave05, Barras05, Py10]

Essentiality data for sufC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of SufBC2D Fe-S cluster scaffold complex: SufD component of SufBCD Fe-S cluster scaffold complex

Synonyms: YnhC, SufD

Gene: sufD Accession Numbers: G6907 (EcoCyc), b1681, ECK1677

Locations: cytosol

Sequence Length: 423 AAs

Molecular Weight: 46.823 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Kri14]
GO:0016226 - iron-sulfur cluster assembly Inferred from experiment Inferred by computational analysis [GOA01, Saini10]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Wollers10, Wada09, Layer07, Butland05]
Cellular Component: GO:0005829 - cytosol

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

Unification Links: DIP:DIP-10940N , EcoliWiki:b1681 , Mint:MINT-7290848 , ModBase:P77689 , PR:PRO_000024008 , Pride:P77689 , Protein Model Portal:P77689 , RefSeq:NP_416196 , SMR:P77689 , String:511145.b1681 , UniProt:P77689

Relationship Links: InterPro:IN-FAMILY:IPR000825 , InterPro:IN-FAMILY:IPR011542 , PDB:Structure:1VH4 , PDB:Structure:2ZU0 , Pfam:IN-FAMILY:PF01458

Summary:
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. SufD is a component of the SufBC2D Fe-S cluster assembly scaffold complex. Both SufC and SufD are required for Fe-S cluster formation on SufB in vivo. The SufD subunit is dispensible for sulfur transfer in vivo, but it is required for the acquisition of iron [Saini10].

A crystal structure of the SufC2-SubD2 complex has been determined at 2.2 Å resolution [Wada09].

A sufD, sufS or fhuF mutant exhibits a defect in utilization of a ferrioxamine B iron source [Patzer99]. A sufD mutant exhibits unstable FhuF, compared to wild type, which precludes overproduction of FhuF [Patzer99]. A sufABCDSE operon deletion mutation leads to increased sensitivity to superoxide-generating agents [Lee04a], 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]. 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].

Expression of sufA, the first gene in the sufABCDSE operon, is induced by superoxide generators and hydrogen peroxide [Lee04a]. Regulation occurs via the iron-dependent Fur repressor [Patzer99], OxyR, IHF, and IscR [Lee04a, Yeo06, Lee08].

sufD shows differential codon adaptation, resulting in differential translation efficiency signatures, in aerotolerant compared to obligate anaerobic microbes. It was therefore predicted to play a role in the oxidative stress response. A sufD deletion mutant was shown to be more sensitive than wild-type specifically to hydrogen peroxide exposure, but not other stresses [Kri14].

Reviews: [Johnson05, Fontecave05, Barras05, Py10]

Essentiality data for sufD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

References

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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

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

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

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

Kitaoka06: Kitaoka S, Wada K, Hasegawa Y, Minami Y, Fukuyama K, Takahashi Y (2006). "Crystal structure of Escherichia coli SufC, an ABC-type ATPase component of the SUF iron-sulfur cluster assembly machinery." FEBS Lett 580(1);137-43. PMID: 16364320

Kri14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Layer07: Layer G, Gaddam SA, Ayala-Castro CN, Ollagnier-de Choudens S, Lascoux D, Fontecave M, Outten FW (2007). "SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly." J Biol Chem 282(18);13342-50. PMID: 17350958

Lee04a: 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

Lee08: 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

Loiseau03: Loiseau L, Ollagnier-de-Choudens S, Nachin L, Fontecave M, Barras F (2003). "Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase." J Biol Chem 278(40);38352-9. PMID: 12876288

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

Nachin01: Nachin L, El Hassouni M, Loiseau L, Expert D, Barras F (2001). "SoxR-dependent response to oxidative stress and virulence of Erwinia chrysanthemi: the key role of SufC, an orphan ABC ATPase." Mol Microbiol 39(4);960-72. PMID: 11251816

Outten03: Outten FW, Wood MJ, Munoz FM, Storz G (2003). "The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in E. coli." J Biol Chem 278(46):45713-9. PMID: 12941942

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

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

Rangachari02: Rangachari K, Davis CT, Eccleston JF, Hirst EM, Saldanha JW, Strath M, Wilson RJ (2002). "SufC hydrolyzes ATP and interacts with SufB from Thermotoga maritima." FEBS Lett 2002;514(2-3);225-8. PMID: 11943156

Richardson03: Richardson DR (2003). "The biogenesis of [Fe-S] clusters: the role of the unorthodox ABC ATPase, SufC, and the wider implications for understanding iron metabolism." Redox Rep 8(3);125-7. PMID: 12935308

Saini10: Saini A, Mapolelo DT, Chahal HK, Johnson MK, Outten FW (2010). "SufD and SufC ATPase activity are required for iron acquisition during in vivo Fe-S cluster formation on SufB." Biochemistry 49(43);9402-12. PMID: 20857974

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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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Wada09: Wada K, Sumi N, Nagai R, Iwasaki K, Sato T, Suzuki K, Hasegawa Y, Kitaoka S, Minami Y, Outten FW, Takahashi Y, Fukuyama K (2009). "Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of the SufC(2)-SufD(2) complex." J Mol Biol 387(1);245-58. PMID: 19361433

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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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, biocyc11.