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Escherichia coli K-12 substr. MG1655 Enzyme: diguanylate cyclase



Gene: ycdT Accession Numbers: G6532 (EcoCyc), b1025, ECK1015

Regulation Summary Diagram: ?

Summary:
YcdT is a diguanylate cyclase that regulates motility; the effect on motility is probably mediated by the second messenger c-di-GMP [Jonas08].

YcdT has similarity to the HmsT protein encoded by the Yersinia pestis hmsHFRST gene cluster, which is involved in plague transmission [Jones99a].

Membrane topology predictions using experimentally determined C terminus locations indicate that YcdT has 8 transmembrane helices and the C-terminus is located in the cytoplasm [Rapp04]. The transmembrane domains are followed by a C-terminal GGDEF domain [Jonas08].

Overexpression of YcdT represses swimming behavior [Jonas08]. Expression of YcdT is repressed by CsrA, which interacts directly with the 5' leader sequence of the ycdT mRNA and modulates the stability of the message [Jonas08].

Locations: inner membrane

Map Position: [1,092,099 -> 1,093,457] (23.54 centisomes)
Length: 1359 bp / 452 aa

Molecular Weight of Polypeptide: 51.783 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003472 , EchoBASE:EB3626 , EcoGene:EG13866 , EcoliWiki:b1025 , OU-Microarray:b1025 , PortEco:ycdT , Pride:P75908 , Protein Model Portal:P75908 , RefSeq:NP_415544 , RegulonDB:G6532 , SMR:P75908 , String:511145.b1025 , UniProt:P75908

Relationship Links: InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR001054 , Pfam:IN-FAMILY:PF00990 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 117 (13 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Jonas08, UniProtGOA11, GOA01a]
GO:0051271 - negative regulation of cellular component movement Inferred from experiment [Jonas08]
Molecular Function: GO:0052621 - diguanylate cyclase activity Inferred from experiment Inferred by computational analysis [GOA01a, Jonas08]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05, Rapp04]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)

Essentiality data for ycdT 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 ? 09-Sep-2008 by Keseler I , SRI International


Enzymatic reaction of: diguanylate cyclase

EC Number: 2.7.7.65

2 GTP <=> cyclic di-3',5'-guanylate + 2 diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

T(opt): 30 °C [BRENDA14, Tuckerman09]

pH(opt): 7.5 [BRENDA14, Zahringer11]


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 8 -> 28
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 46 -> 66
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 75 -> 95
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 112 -> 132
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Extrinsic-Sequence-Variant 130
[UniProt10]
Alternate sequence: A → V; UniProt: (in strain: K12 / W3110 / ATCC 27325 / DSM 5911);
Transmembrane-Region 149 -> 169
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 196 -> 216
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 220 -> 240
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 255 -> 275
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 310 -> 445
[UniProt09]
UniProt: GGDEF;
Metal-Binding-Site 318
[UniProt10]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 323
[UniProt10]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 326
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 335
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 359 -> 360
[Jonas08, UniProt11]
Alternate sequence: GG → AA; UniProt: Cells overexpressing this mutant are no longer swimming suppressed.
Metal-Binding-Site 361
[UniProt10]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 361
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

Jonas08: Jonas K, Edwards AN, Simm R, Romeo T, Romling U, Melefors O (2008). "The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins." Mol Microbiol 70(1);236-57. PMID: 18713317

Jones99a: Jones HA, Lillard JW, Perry RD (1999). "HmsT, a protein essential for expression of the haemin storage (Hms+) phenotype of Yersinia pestis." Microbiology 145 ( Pt 8);2117-28. PMID: 10463178

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

Rapp04: Rapp M, Drew D, Daley DO, Nilsson J, Carvalho T, Melen K, De Gier JW, Von Heijne G (2004). "Experimentally based topology models for E. coli inner membrane proteins." Protein Sci 13(4);937-45. PMID: 15044727

Tuckerman09: Tuckerman JR, Gonzalez G, Sousa EH, Wan X, Saito JA, Alam M, Gilles-Gonzalez MA (2009). "An Oxygen-Sensing Diguanylate Cyclase and Phosphodiesterase Couple for c-di-GMP Control." Biochemistry 48(41):9764-74. PMID: 19764732

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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."

Zahringer11: Zahringer F, Massa C, Schirmer T (2011). "Efficient enzymatic production of the bacterial second messenger c-di-GMP by the diguanylate cyclase YdeH from E. coli." Appl Biochem Biotechnol 163(1);71-9. PMID: 20582742


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 18.5 on Sun Dec 21, 2014, biocyc14.