Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015

Escherichia coli K-12 substr. MG1655 Protein: glutaredoxin 4

Gene: grxD Accession Numbers: EG12181 (EcoCyc), b1654, ECK1650

Synonyms: ydhD, Grx4

Regulation Summary Diagram: ?

Regulation summary diagram for grxD

Component of: Grx4-BolA complex (summary available)

Subunit composition of glutaredoxin 4 = [GrxD]2
         glutaredoxin 4 = GrxD

Grx4 belongs to the family of monothiol glutaredoxins. The dimeric Grx4 can act as a scaffold protein, transferring an intact [2Fe-2S] cluster to the model acceptor protein ferredoxin [Yeung11].

Oxidized Grx4 can be reduced by the thioredoxin system or glutaredoxin 1. Grx4 is not active in the standard glutaredoxin assay [Fernandes05].

A solution structure of the reduced form of Grx4 has been determined [Fladvad05]. A crystal structure of the Grx4 dimer coordinating a [2Fe-2S] cluster at the dimer interface has been solved. This arrangement suggests that Grx4 has to undergo a conformational change to release the [2Fe-2S] cluster [Iwema09].

Physical [Bolstad10a, Bolstad10] and genetic [Butland08] interactions with iron-sulfur cluster assembly proteins suggest that Grx4 acts as a scaffold and/or transfer protein for iron-sulfur clusters to the SUF and CSD systems. Both GrxD and NfuA interact with MiaB. NfuA, but not GrxD, can transfer a 4Fe-4S cluster to apo-MiaB in vitro, and both proteins affect MiaB activity in vivo [Boutigny13].

Grx4 is an abundant protein that is upregulated upon iron depletion and during stationary phase; the increased expression is dependent on ppGpp [Fernandes05]. A grxD null mutant could not be obtained by [Fernandes05]. grxD has previously been reported to be essential for aerobic growth in rich media [Gerdes03]. However, a grxD mutant is available as part of the Keio collection [Baba06] and was shown to be sensitive to iron depletion [Yeung11].

Reviews: [Toledano07, Meyer09, Li12a, Roche13]

Locations: cytosol

Map Position: [1,731,778 <- 1,732,125] (37.33 centisomes, 134°)
Length: 348 bp / 115 aa

Molecular Weight of Polypeptide: 12.879 kD (from nucleotide sequence), 17.8 kD (experimental) [Yeung11 ]

Molecular Weight of Multimer: 37.6 kD (experimental) [Yeung11]

Unification Links: ASAP:ABE-0005527 , DIP:DIP-11729N , EchoBASE:EB2098 , EcoGene:EG12181 , EcoliWiki:b1654 , Mint:MINT-1258030 , ModBase:P0AC69 , OU-Microarray:b1654 , PortEco:grxD , PR:PRO_000022842 , Pride:P0AC69 , Protein Model Portal:P0AC69 , RefSeq:NP_416171 , RegulonDB:EG12181 , SMR:P0AC69 , String:511145.b1654 , UniProt:P0AC69

Relationship Links: InterPro:IN-FAMILY:IPR002109 , InterPro:IN-FAMILY:IPR004480 , InterPro:IN-FAMILY:IPR012336 , InterPro:IN-FAMILY:IPR014434 , Panther:IN-FAMILY:PTHR10293 , PDB:Structure:1YKA , PDB:Structure:2WCI , Pfam:IN-FAMILY:PF00462 , Prosite:IN-FAMILY:PS51354

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for grxD

GO Terms:

Biological Process: GO:0045454 - cell redox homeostasis Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Boutigny13, Yeung11, Bolstad10a, Bolstad10, Butland05]
GO:0042803 - protein homodimerization activity Inferred from experiment [Yeung11]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Iwema09]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
GO:0015035 - protein disulfide oxidoreductase activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers thioredoxin, glutaredoxin

Essentiality data for grxD 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]
Yes [Feist07, Comment 3]

Created 29-Jul-2009 by Keseler I , SRI International
Last-Curated ? 19-Apr-2013 by Keseler I , SRI International

Subunit of: Grx4-BolA complex

Subunit composition of Grx4-BolA complex = [BolA][GrxD]
         BolA DNA-binding transcriptional dual regulator = BolA (extended summary available)
         glutaredoxin 4 = GrxD (extended summary available)

The heterodimeric Grx4-BolA complex can bind an intact [2Fe-2S] cluster and transfer it to the model acceptor protein ferredoxin, although much less efficiently than the Grx4 homodimer [Yeung11].

Created 14-Sep-2011 by Keseler I , SRI International
Last-Curated ? 14-Sep-2011 by Keseler I , SRI International

Sequence Features

Protein sequence of glutaredoxin 4 with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Conserved-Region 5 -> 107
UniProt: Glutaredoxin;
Acetylation-Modification 7
Amino-Acid-Sites-That-Bind 22
[Iwema09, UniProt15]
UniProt: Glutathione.
Metal-Binding-Site 30
UniProt: Iron-sulfur (2Fe-2S); shared with dimeric partner.
Amino-Acid-Sites-That-Bind 59
[Iwema09, UniProt15]
UniProt: Glutathione.
Amino-Acid-Sites-That-Bind 71
[Iwema09, UniProt15]
UniProt: Glutathione; via amide nitrogen and carbonyl oxygen.
Protein-Segment 84 -> 85
UniProt: Glutathione binding; Sequence Annotation Type: region of interest;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b1654 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12181; 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

Bolstad10: Bolstad HM, Wood MJ (2010). "An in vivo method for characterization of protein interactions within sulfur trafficking systems of E. coli." J Proteome Res 9(12);6740-51. PMID: 20936830

Bolstad10a: Bolstad HM, Botelho DJ, Wood MJ (2010). "Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system." J Proteome Res 9(10);5358-69. PMID: 20734996

Boutigny13: Boutigny S, Saini A, Baidoo EE, Yeung N, Keasling JD, Butland G (2013). "Physical and Functional Interactions of a Monothiol Glutaredoxin and an Iron Sulfur Cluster Carrier Protein with the Sulfur-donating Radical S-Adenosyl-L-methionine Enzyme MiaB." J Biol Chem 288(20);14200-11. PMID: 23543739

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

Butland08: Butland G, Babu M, Diaz-Mejia JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A (2008). "eSGA: E. coli synthetic genetic array analysis." Nat Methods 5(9);789-95. PMID: 18677321

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Fernandes05: Fernandes AP, Fladvad M, Berndt C, Andresen C, Lillig CH, Neubauer P, Sunnerhagen M, Holmgren A, Vlamis-Gardikas A (2005). "A novel monothiol glutaredoxin (Grx4) from Escherichia coli can serve as a substrate for thioredoxin reductase." J Biol Chem 280(26);24544-52. PMID: 15833738

Fladvad05: Fladvad M, Bellanda M, Fernandes AP, Mammi S, Vlamis-Gardikas A, Holmgren A, Sunnerhagen M (2005). "Molecular mapping of functionalities in the solution structure of reduced Grx4, a monothiol glutaredoxin from Escherichia coli." J Biol Chem 280(26);24553-61. PMID: 15840565

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

GOA01a: 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

Iwema09: Iwema T, Picciocchi A, Traore DA, Ferrer JL, Chauvat F, Jacquamet L (2009). "Structural basis for delivery of the intact [Fe2S2] cluster by monothiol glutaredoxin." Biochemistry 48(26);6041-3. PMID: 19505088

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

Li12a: Li H, Outten CE (2012). "Monothiol CGFS glutaredoxins and BolA-like proteins: [2Fe-2S] binding partners in iron homeostasis." Biochemistry 51(22);4377-89. PMID: 22583368

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

Meyer09: Meyer Y, Buchanan BB, Vignols F, Reichheld JP (2009). "Thioredoxins and glutaredoxins: unifying elements in redox biology." Annu Rev Genet 43;335-67. PMID: 19691428

Roche13: Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F (2013). "Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity." Biochim Biophys Acta 1827(3);455-69. PMID: 23298813

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Toledano07: Toledano MB, Kumar C, Le Moan N, Spector D, Tacnet F (2007). "The system biology of thiol redox system in Escherichia coli and yeast: differential functions in oxidative stress, iron metabolism and DNA synthesis." FEBS Lett 581(19);3598-607. PMID: 17659286

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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

Yeung11: Yeung N, Gold B, Liu NL, Prathapam R, Sterling HJ, Willams ER, Butland G (2011). "The E. coli monothiol glutaredoxin GrxD forms homodimeric and heterodimeric FeS cluster containing complexes." Biochemistry 50(41);8957-69. PMID: 21899261

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

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

Report Errors or Provide Feedback
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 19.0 on Sat Aug 29, 2015, biocyc12.