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Escherichia coli K-12 substr. MG1655 Enzyme: KpLE2 phage-like element; 2-dehydro-3-deoxy-D-pentonate aldolase



Gene: yjhH Accession Numbers: G7911 (EcoCyc), b4298, ECK4287

Regulation Summary Diagram: ?

Summary:
YjhH appears to be a 2-dehydro-3-deoxy-D-pentonate aldolase [Liu13].

A yjhH yagE double mutant can not use D-xylonate as the sole source of carbon, and crude cell extracts do not contain 2-dehydro-3-deoxy-D-pentonate aldolase activity. Both phenotypes are complemented by providing yjhH on a plasmid [Liu13].

ArcA appears to activate yjhH gene expression under anaerobiosis. Two putative ArcA binding sites were identified 211 and 597 bp upstream of this gene [Salmon05], but no promoter upstream of it has been identified.

Locations: cytosol

Map Position: [4,522,128 <- 4,523,033] (97.47 centisomes)
Length: 906 bp / 301 aa

Molecular Weight of Polypeptide: 32.722 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014089 , DIP:DIP-12622N , EchoBASE:EB2438 , EcoGene:EG12550 , EcoliWiki:b4298 , Mint:MINT-1301013 , ModBase:P39359 , OU-Microarray:b4298 , PortEco:yjhH , Protein Model Portal:P39359 , RefSeq:NP_418718 , RegulonDB:G7911 , SMR:P39359 , String:511145.b4298 , UniProt:P39359

Relationship Links: InterPro:IN-FAMILY:IPR002220 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR020624 , InterPro:IN-FAMILY:IPR020625 , Panther:IN-FAMILY:PTHR12128 , Pfam:IN-FAMILY:PF00701 , Prints:IN-FAMILY:PR00146 , Prosite:IN-FAMILY:PS00665 , Prosite:IN-FAMILY:PS00666

In Paralogous Gene Group: 81 (7 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0046176 - aldonic acid catabolic process Inferred from experiment [Liu13]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0047440 - 2-dehydro-3-deoxy-D-pentonate aldolase activity Inferred from experiment [Liu13]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism unassigned reversible reactions

Essentiality data for yjhH 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:
Curated 27-Jan-2006 by Shearer A , SRI International
Last-Curated ? 13-Nov-2013 by Keseler I , SRI International


Enzymatic reaction of: 2-dehydro-3-deoxy-D-pentonate aldolase

EC Number: 4.1.2.28

2-dehydro-3-deoxy-D-arabinonate <=> glycolaldehyde + pyruvate

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

Reversibility of this reaction is unspecified.


Sequence Features

Feature Class Location Citations Comment
Active-Site 46
[UniProt11]
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity.
Active-Site 109
[UniProt11]
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity.
Active-Site 135
[UniProt11]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity.
Active-Site 164
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
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

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, 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

Liu13: Liu H, Ramos KR, Valdehuesa KN, Nisola GM, Lee WK, Chung WJ (2013). "Biosynthesis of ethylene glycol in Escherichia coli." Appl Microbiol Biotechnol 97(8);3409-17. PMID: 23233208

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Other References Related to Gene Regulation

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 Nov 23, 2014, BIOCYC14B.