Escherichia coli K-12 substr. MG1655 Protein: transthyretin-related protein

Gene: yedX Accession Numbers: G7058 (EcoCyc), b1970, ECK1966

Regulation Summary Diagram

Regulation summary diagram for yedX

Subunit composition of transthyretin-related protein = [YedX]4
         conserved protein = YedX

YedX belongs to the family of transthyretin-related proteins (TRP). Transthyretin is a transport protein in extracellular fluids of vertebrates, where it distributes thyroid hormones [Richardson02].

YedX contains a cleaved signal sequence and may thus be located in the periplasm. The protein is a tetramer in solution. E. coli YedX does not bind the thyroid hormones thyroxine and triiodo-thyronine [Eneqvist03].

Crystal structures of YedX have been determined at 1.65 and 2.1 Å resolution. The structures are similar to eukaryotic transthyretins. Zinc ions are located at the putative ligand binding site, although zinc is absent from the purified recombinant protein [Lundberg06].

Review: [Richardson02]

Locations: periplasmic space

Map Position: [2,036,980 -> 2,037,393] (43.9 centisomes, 158°)
Length: 414 bp / 137 aa

Molecular Weight of Polypeptide: 15.46 kD (from nucleotide sequence)

Molecular Weight of Multimer: 50 kD (experimental) [Eneqvist03]

pI: 8.4 [Eneqvist03]

Unification Links: ASAP:ABE-0006537, DIP:DIP-11854N, EchoBASE:EB3799, EcoGene:EG14046, EcoliWiki:b1970, ModBase:P76341, OU-Microarray:b1970, PortEco:yedX, Protein Model Portal:P76341, RefSeq:NP_416479, RegulonDB:G7058, SMR:P76341, String:511145.b1970, UniProt:P76341

Relationship Links: InterPro:IN-FAMILY:IPR000895, InterPro:IN-FAMILY:IPR014306, InterPro:IN-FAMILY:IPR023416, InterPro:IN-FAMILY:IPR023418, InterPro:IN-FAMILY:IPR023419, PDB:Structure:2G2N, PDB:Structure:2G2P, PDB:Structure:2IGL, Pfam:IN-FAMILY:PF00576, Prints:IN-FAMILY:PR00189, Prosite:IN-FAMILY:PS00768, Prosite:IN-FAMILY:PS00769, Smart:IN-FAMILY:SM00095

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for yedX

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006144 - purine nucleobase metabolic process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Inferred by computational analysisGO:0033971 - hydroxyisourate hydrolase activity [GOA01, GOA01a]
Cellular Component:
Inferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09]
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a]

Gene Class: ORFsConserved-ORFs

Essentiality data for yedX knockouts:

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

Created 31-May-2006 by Keseler I, SRI International
Last-Curated 31-May-2006 by Keseler I, SRI International

Sequence Features

Protein sequence of conserved protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
Inferred from experiment[Eneqvist03, Eneqvist03]
Chain 24 -> 137
Author statement[UniProt15]
UniProt: 5-hydroxyisourate hydrolase.
Pfam PF00576 29 -> 136
Inferred by computational analysis[Finn14]
Transthyretin : HIUase/Transthyretin family
Amino-Acid-Sites-That-Bind 32
Inferred by computational analysis[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 70
Inferred by computational analysis[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 134
Inferred by computational analysis[UniProt15]
UniProt: Substrate.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


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


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

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

Eneqvist03: Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE (2003). "The transthyretin-related protein family." Eur J Biochem 270(3);518-32. PMID: 12542701

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

Lundberg06: Lundberg E, Backstrom S, Sauer UH, Sauer-Eriksson AE (2006). "The transthyretin-related protein: Structural investigation of a novel protein family." J Struct Biol 155(3):445-57. PMID: 16723258

Richardson02: Richardson SJ (2002). "The evolution of transthyretin synthesis in vertebrate liver, in primitive eukaryotes and in bacteria." Clin Chem Lab Med 40(12);1191-9. PMID: 12553419

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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."

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

Urano15: Urano H, Umezawa Y, Yamamoto K, Ishihama A, Ogasawara H (2015). "Cooperative regulation of the common target genes between H2O2-sensing YedVW and Cu2+-sensing CusSR in Escherichia coli." Microbiology 161(Pt 4);729-38. PMID: 25568260

Yang12a: Yang C, Huang TW, Wen SY, Chang CY, Tsai SF, Wu WF, Chang CH (2012). "Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli." PLoS One 7(10);e47314. PMID: 23071782

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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 Pathway Tools version 19.5 (software by SRI International) on Sat Nov 28, 2015, biocyc13.