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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Enzyme: L-rhamnose mutarotase



Gene: rhaM Accession Numbers: EG11865 (EcoCyc), b3901, ECK3894

Synonyms: yiiL

Regulation Summary Diagram: ?

Subunit composition of L-rhamnose mutarotase = [RhaM]2
         L-rhamnose mutarotase = RhaM

Summary:
Utilizing NMR techniques, RhaM was shown to catalyze the anomeric conversion of rhamnose [Ryu04]. The enzyme has a preference for binding the β-anomer [Ryu05].

A crystal structure of RhaM in complex with L-rhamnose was solved at 1.8 Å resolution. Analysis of the catalytic activity of mutants in predicted active site residues allowed the authors to propose a possible catalytic mechanism [Ryu05].

A rhaM deletion mutant has a decreased growth rate when grown on low concentrations of L-rhamnose [Ryu05].

Locations: cytosol

Map Position: [4,091,147 <- 4,091,461] (88.18 centisomes)
Length: 315 bp / 104 aa

Molecular Weight of Polypeptide: 12.265 kD (from nucleotide sequence)

Molecular Weight of Multimer: 23.7 kD (experimental) [Ryu05]

Unification Links: ASAP:ABE-0012729 , EchoBASE:EB1811 , EcoGene:EG11865 , EcoliWiki:b3901 , OU-Microarray:b3901 , PortEco:rhaM , PR:PRO_000023736 , Protein Model Portal:P32156 , RefSeq:NP_418337 , RegulonDB:EG11865 , SMR:P32156 , String:511145.b3901 , UniProt:P32156

Relationship Links: InterPro:IN-FAMILY:IPR008000 , InterPro:IN-FAMILY:IPR011008 , InterPro:IN-FAMILY:IPR013448 , PDB:Structure:1X8D , Pfam:IN-FAMILY:PF05336

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019301 - rhamnose catabolic process Inferred from experiment [Ryu05]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0019299 - rhamnose metabolic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01]
Molecular Function: GO:0016857 - racemase and epimerase activity, acting on carbohydrates and derivatives Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Ryu04]
GO:0042803 - protein homodimerization activity Inferred from experiment [Ryu05]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01]

MultiFun Terms: metabolism carbon utilization

Essentiality data for rhaM 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:
Created 06-Nov-2007 by Keseler I , SRI International
Last-Curated ? 06-Nov-2007 by Keseler I , SRI International


Enzymatic reaction of: L-rhamnose mutarotase

EC Number: 5.1.3.-

α-L-rhamnopyranose <=> β-L-rhamnopyranose

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: superpathway of fucose and rhamnose degradation , L-rhamnose degradation I


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 18
[Ryu05, UniProt11]
Alternate sequence: Y → F; UniProt: Loss of mutarotase activity.
Amino-Acid-Sites-That-Bind 18
[UniProt10]
UniProt: Substrate;
Active-Site 22
[UniProt10a]
UniProt: Proton donor; Non-Experimental Qualifier: probable;
Amino-Acid-Sites-That-Bind 41
[UniProt10]
UniProt: Substrate;
Protein-Segment 76 -> 77
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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 b3901 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11865; confirmed by SwissProt match.


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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Ryu04: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C (2004). "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." J Biol Chem 279(24);25544-8. PMID: 15060078

Ryu05: Ryu KS, Kim JI, Cho SJ, Park D, Park C, Cheong HK, Lee JO, Choi BS (2005). "Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase." J Mol Biol 349(1);153-62. PMID: 15876375

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

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 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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


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 Mon Dec 22, 2014, BIOCYC14B.