DB code: S00245

CATH domain 3.20.20.150 : TIM Barrel Catalytic domain
E.C. 5.3.1.14
CSA 1de6
M-CSA 1de6
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P32170 L-rhamnose isomerase
EC 5.3.1.14
YP_026276.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491547.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF06134 (RhaA)
[Graphical View]

KEGG enzyme name
L-rhamnose isomerase
rhamnose isomerase
L-rhamnose ketol-isomerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P32170 RHAA_ECOLI L-rhamnose = L-rhamnulose. Homotetramer. Cytoplasm (Probable). Binds 1 manganese ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00034 C00038 C00507 C00861
E.C.
Compound Manganese Zinc L-Rhamnose L-Rhamnulose
Type heavy metal heavy metal carbohydrate carbohydrate
ChEBI 18291
35154
29105
62346
17897
PubChem 23930
32051
25310
14461866
1d8wA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Unbound Unbound
1d8wB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Unbound Unbound
1d8wC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Unbound Unbound
1d8wD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Unbound Unbound
1de5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Analogue:RNT Unbound
1de5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Analogue:RNT Unbound
1de5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Analogue:RNT Unbound
1de5D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_ZN Analogue:RNT Unbound
1de6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Bound:_ZN Bound:RNS Unbound
1de6B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Bound:_ZN Bound:RNS Unbound
1de6C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Bound:_ZN Bound:RNS Unbound
1de6D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Bound:_ZN Bound:RNS Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P32170 & literature [4], [5], [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d8wA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1d8wB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1d8wC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1d8wD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de5D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de6B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de6C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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)
1de6D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 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
References Sections No. of steps in catalysis
[3]
Fig.12, Fig.13, p.168-170 7
[4]
p.5464-5465
[5]
Fig.1, p.22903-22905
[6]
Figure 11, p.928
[7]
Scheme 11, Scheme 12, p.101

References
[1]
Resource
Comments
Medline ID
PubMed ID
Journal Methods Enzymol
Year 1966
Volume 9
Pages 579-82
Authors Domagk GF, Zech R
Title L-Rhamnose isomerase
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1650346
Journal J Bacteriol
Year 1991
Volume 173
Pages 5144-50
Authors Badia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Aguilar J
Title L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2006134
Journal Proteins
Year 1991
Volume 9
Pages 153-73
Authors Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL
Title A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1610792
Journal Biochemistry
Year 1992
Volume 31
Pages 5459-66
Authors Lambeir AM, Lauwereys M, Stanssens P, Mrabet NT, Snauwaert J, van Tilbeurgh H, Matthyssens G, Lasters I, De Maeyer M, Wodak SJ, et al
Title Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of the xylose binding site.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7559425
Journal J Biol Chem
Year 1995
Volume 270
Pages 22895-906
Authors Whitaker RD, Cho Y, Cha J, Carrell HL, Glusker JP, Karplus PA, Batt CA
Title Probing the roles of active site residues in D-xylose isomerase.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID
PubMed ID 10891278
Journal J Mol Biol
Year 2000
Volume 300
Pages 917-33
Authors Korndorfer IP, Fessner WD, Matthews BW
Title The 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 PDB 1d8w 1de5 1de6
Related UniProtKB P32170
[7]
Resource
Comments
Medline ID
PubMed ID
Journal Top Curr Chem
Year 2001
Volume 215
Pages 77-114
Authors Hausler H, Stutz AE
Title D-xylose (D-glucose) isomerase and related enzymes in carbohydrate synthesis.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 15184124
Journal Appl Environ Microbiol
Year 2004
Volume 70
Pages 3298-304
Authors Leang K, Takada G, Ishimura A, Okita M, Izumori K
Title Cloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15342115
Journal Biochim Biophys Acta
Year 2004
Volume 1674
Pages 68-77
Authors Leang K, Takada G, Fukai Y, Morimoto K, Granstrom TB, Izumori K
Title Novel reactions of L-rhamnose isomerase from Pseudomonas stutzeri and its relation with D-xylose isomerase via substrate specificity.
Related PDB
Related UniProtKB

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]).

Created Updated
2005-07-08 2009-02-26