EzCatDB: S00245

DB codeS00245
CATH domainDomain 13.20.20.150Catalytic domain
E.C.5.3.1.14
CSA1de6


Enzyme Name
Swiss-protKEGG

P32170
Protein nameL-rhamnose isomeraseL-rhamnose isomerase
rhamnose isomerase
L-rhamnose ketol-isomerase
SynonymsEC 5.3.1.14

KEGG pathways
MAP codePathways
MAP00051Fructose and mannose metabolism

Swiss-prot:Accession NumberP32170
Entry nameRHAA_ECOLI
ActivityL-rhamnose = L-rhamnulose.
SubunitHomotetramer.
Subcellular locationCytoplasm (Probable).
CofactorBinds 1 manganese ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00034C00038C00507C00861
CompoundManganeseZincL-RhamnoseL-Rhamnulose
Typeheavy metalheavy metalcarbohydratecarbohydrate
1d8wAUnboundBound:_ZNUnboundUnbound
1d8wBUnboundBound:_ZNUnboundUnbound
1d8wCUnboundBound:_ZNUnboundUnbound
1d8wDUnboundBound:_ZNUnboundUnbound
1de5AUnboundBound:_ZNAnalogue:RNTUnbound
1de5BUnboundBound:_ZNAnalogue:RNTUnbound
1de5CUnboundBound:_ZNAnalogue:RNTUnbound
1de5DUnboundBound:_ZNAnalogue:RNTUnbound
1de6ABound:_MNBound:_ZNBound:RNSUnbound
1de6BBound:_MNBound:_ZNBound:RNSUnbound
1de6CBound:_MNBound:_ZNBound:RNSUnbound
1de6DBound:_MNBound:_ZNBound:RNSUnbound

Active-site residues
resource
Swiss-prot;P32170 & literature [4], [5], [6]
pdbCatalytic residuesCofactor-binding residues
1d8wATRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1d8wBTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1d8wCTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1d8wDTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de5ATRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de5BTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de5CTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de5DTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de6ATRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de6BTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de6CTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)
1de6DTRP 193;LYS 236;HIS 270;ASP 302
HIS 270;ASP 302;ASP 304(Manganese binding);GLU 234;ASP 267;HIS 294;ASP 334(Zinc binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.12, Fig.13, p.168-1707
[4]p.5464-5465
[5]Fig.1, p.22903-22905
[6]Figure 11, p.928
[7]Scheme 11, Scheme 12, p.101

references
[1]
JournalMethods Enzymol
Year1966
Volume9
Pages579-82
AuthorsDomagk GF, Zech R
TitleL-Rhamnose isomerase
[2]
PubMed ID1650346
JournalJ Bacteriol
Year1991
Volume173
Pages5144-50
AuthorsBadia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Aguilar J
TitleL-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose.
[3]
PubMed ID2006134
JournalProteins
Year1991
Volume9
Pages153-73
AuthorsWhitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL
TitleA metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose.
[4]
PubMed ID1610792
JournalBiochemistry
Year1992
Volume31
Pages5459-66
AuthorsLambeir AM, Lauwereys M, Stanssens P, Mrabet NT, Snauwaert J, van Tilbeurgh H, Matthyssens G, Lasters I, De Maeyer M, Wodak SJ, et al
TitleProtein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of the xylose binding site.
[5]
PubMed ID7559425
JournalJ Biol Chem
Year1995
Volume270
Pages22895-906
AuthorsWhitaker RD, Cho Y, Cha J, Carrell HL, Glusker JP, Karplus PA, Batt CA
TitleProbing the roles of active site residues in D-xylose isomerase.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
PubMed ID10891278
JournalJ Mol Biol
Year2000
Volume300
Pages917-33
AuthorsKorndorfer IP, Fessner WD, Matthews BW
TitleThe structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution.
Related PDB1d8w,1de5,1de6
Related Swiss-protP32170
[7]
JournalTop Curr Chem
Year2001
Volume215
Pages77-114
AuthorsHausler H, Stutz AE
TitleD-xylose (D-glucose) isomerase and related enzymes in carbohydrate synthesis.
[8]
PubMed ID15184124
JournalAppl Environ Microbiol
Year2004
Volume70
Pages3298-304
AuthorsLeang K, Takada G, Ishimura A, Okita M, Izumori K
TitleCloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli.
[9]
PubMed ID15342115
JournalBiochim Biophys Acta
Year2004
Volume1674
Pages68-77
AuthorsLeang K, Takada G, Fukai Y, Morimoto K, Granstrom TB, Izumori K
TitleNovel reactions of L-rhamnose isomerase from Pseudomonas stutzeri and its relation with D-xylose isomerase via substrate specificity.

comments
Although this enzyme binds a zinc ion at the active site, it is not directly involved in catalysis, and might be replaced by different metal ion in vivo (see [6]). In contrast, manganese ion is an essential cofactor for catalysis.
The active site structure of this enzyme complexed with substrate is similar but slightly different from that of the homologous enzyme, xylose isomerase (4xis in PDB). It is not clear whether detailed mechanism is the same as that of the counterpart.
According to the literature [6], this enzyme catalyzes the following reactions:
(A) Ring opening of rhamnose (Eliminative double-bond formation).
The mechanism for this reaction has not been elucidated yet.
(B) Isomerization; Shift of double-bond.
This reaction involves hydride shift from the C2 atom to the C1 atom. The hydrophobic environment around these atoms, which is formed by Trp193, seems to facilitate this hydride shift. In the active site of xylose isomerase (PDB;4xis), a catalytic water, bound to manganese ion, is observed. However, the active site of this enzyme does not show such a catalytic water (see 1de6). If there is no catalytic water, Asp302 and His270 might contribute to the reaction, along with Lys236 (see [6]).

createdupdated
2005-07-082009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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