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Escherichia coli K-12 substr. MG1655 Polypeptide: SufD component of SufBCD Fe-S cluster scaffold complex



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

Synonyms: ynhC

Regulation Summary Diagram: ?

Component of: SufBC2D Fe-S cluster scaffold complex (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. 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 [Krisko14].

Reviews: [Johnson05, Fontecave05, Barras05, Py10]

Gene Citations: [Zheng01]

Locations: cytosol

Map Position: [1,758,544 <- 1,759,815] (37.9 centisomes)
Length: 1272 bp / 423 aa

Molecular Weight of Polypeptide: 46.823 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005617 , DIP:DIP-10940N , EchoBASE:EB3721 , EcoGene:EG13963 , EcoliWiki:b1681 , Mint:MINT-7290848 , ModBase:P77689 , OU-Microarray:b1681 , PortEco:sufD , PR:PRO_000024008 , Pride:P77689 , Protein Model Portal:P77689 , RefSeq:NP_416196 , RegulonDB:G6907 , 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

In Paralogous Gene Group: 330 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Krisko14]
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

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]

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


Subunit of: 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]

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


Sequence Features

Feature Class Location Citations
Cleavage-of-Initial-Methionine 1
[Layer07]


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

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

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

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."

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

Krisko14: 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

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

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

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

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

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

Wollers10: Wollers S, Layer G, Garcia-Serres R, Signor L, Clemancey M, Latour JM, Fontecave M, Ollagnier de Choudens S (2010). "Iron-sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor." J Biol Chem 285(30);23331-41. PMID: 20460376

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

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

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

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
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, BIOCYC13A.