L-rhamnose isomerase
This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism.
The enzyme contains two divalent metal ions located at different metal-binding sites within the active site. The enzyme binds the closed ring form of the substrate and catalyses ring opening to generate a form of open-chain conformation that is coordinated to one of the metal sites.
Reference Protein and Structure
- Sequence
-
P32170
(5.3.1.14)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Escherichia coli K-12 (Bacteria)
- PDB
-
1de6
- L-RHAMNOSE ISOMERASE
(2.1 Å)
- Catalytic CATH Domains
-
3.20.20.150
(see all for 1de6)
- Cofactors
- Zinc(2+) (1), Manganese(2+) (1)
Enzyme Reaction (EC:5.3.1.14)
→
Alternative enzyme names: L-rhamnose ketol-isomerase, Rhamnose isomerase,
Enzyme Mechanism
Introduction
Isomerization proceeds via a hydride-shift mechanism. In this mechanism, Asp334 acts as an acid-base catalyst in ring opening, helping to transfer a proton from O2 to O5. After the ring has been opened, the catalytic water molecule (W4) mediates the transfer of a proton from O1 to O2, and a hydride (H1A), shielded by Trp193 from solvent access, attacks C2, producing an aldose with a hydroxyl group (O2) .
Catalytic Residues Roles
| UniProt | PDB* (1de6) | ||
| Asp296 | Asp304(303)A | Forms part of the manganese binding site, although thought to be responsible for the proton abstraction from the catalytic water that initiates the O1 to O2 proton transfer. | metal ligand, proton acceptor, proton donor |
| Glu226, His286, Asp259 | Glu234(233)A, His294(293)A, Asp267(266)A | Forms the zinc binding site. | metal ligand |
| Asp294, Asp259 | Asp302(301)A, Asp267(266)A | Forms manganese binding site. | metal ligand |
| Asp326 | Asp334(333)A | Forms part of the zinc binding site, also thought to be responsible for the initial abstraction of a hydrogen from a catalytic water for the ring opening step of the reaction. | metal ligand, proton acceptor, proton donor |
| His262, Lys228, Trp185 | His270(269)A, Lys236(235)A, Trp193(192)A | Activate the substrate to make hydride transfer favourable. | activator, metal ligand |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
overall reactant used, decyclisation, proton transfer, hydride transfer, overall product formedReferences
- Korndörfer IP et al. (2000), J Mol Biol, 300, 917-933. 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. DOI:10.1006/jmbi.2000.3896. PMID:10891278.
- Prabhu P et al. (2014), FEBS J, 281, 3446-3459. Structure-based studies on the metal binding of two-metal-dependent sugar isomerases. DOI:10.1111/febs.12872. PMID:24925069.
- Yoshida H et al. (2013), FEBS Open Bio, 3, 35-40. Structure ofl-rhamnose isomerase in complex withl-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. DOI:10.1016/j.fob.2012.11.008. PMID:23772372.
- Yoshida H et al. (2010), FEBS J, 277, 1045-1057. Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures. DOI:10.1111/j.1742-4658.2009.07548.x. PMID:20088877.
- Yoshida H et al. (2007), J Mol Biol, 365, 1505-1516. The Structures of l-Rhamnose Isomerase from Pseudomonas stutzeri in Complexes with l-Rhamnose and d-Allose Provide Insights into Broad Substrate Specificity. DOI:10.1016/j.jmb.2006.11.004. PMID:17141803.
Step 1. Asp334 acts as a base via a water molecule to deprotonate O2 this causes the ring to open.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand |
| His270(269)A | metal ligand |
| Asp334(333)A | proton acceptor |
Chemical Components
overall reactant used, decyclisation, proton transfer
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His270(269)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand, proton donor |
Chemical Components
proton transfer
Step 3. Asp304 deprotonates O2 via another water molecule. This causes a hydride shift from C2 to C1.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His270(269)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand |
| Trp193(192)A | activator |
| Lys236(235)A | activator |
| His270(269)A | activator |
| Asp304(303)A | proton acceptor |
Chemical Components
proton transfer, hydride transfer
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His270(269)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand |
| Asp304(303)A | proton donor |
Chemical Components
proton transfer, overall product formed
Download: Introduction
The ene-diol mechanism. In this mechanism two bases transfer a proton from O2 to O1 (thought to be water), and a proton from C1 to C2 (no base identified as yet), respectively, producing ketose from aldose. During the reaction, the ene-diol intermediate is stabilized by the metal ion(s).
Catalytic Residues Roles
| UniProt | PDB* (1de6) | ||
| Asp294, Asp296, Asp259 | Asp302(301)A, Asp304(303)A, Asp267(266)A | Forms manganese binding site. | metal ligand |
| Glu226, His286, Asp259, Asp326 | Glu234(233)A, His294(293)A, Asp267(266)A, Asp334(333)A | Forms zinc binding site. | metal ligand |
| His262, Lys228, Trp185 | His270(269)A, Lys236(235)A, Trp193(192)A | Act to stabilise the substrate and transition states. | activator, metal ligand |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
proton transfer, decyclisation, overall reactant used, assisted keto-enol tautomerisation, overall product formedReferences
- Carrell HL et al. (1989), Proc Natl Acad Sci U S A, 86, 4440-4444. X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator. PMID:2734296.
- Yoshida H et al. (2010), FEBS J, 277, 1045-1057. Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures. DOI:10.1111/j.1742-4658.2009.07548.x. PMID:20088877.
- Kovalevsky AY et al. (2008), Biochemistry, 47, 7595-7597. Hydrogen Location in Stages of an Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure ofd-Xylose Isomerase with Boundd-Xylulose†‡. DOI:10.1021/bi8005434. PMID:18578508.
- Katz AK et al. (2006), Proc Natl Acad Sci U S A, 103, 8342-8347. Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction. DOI:10.1073/pnas.0602598103. PMID:16707576.
Step 1. Asp334 acts as a base via a water molecule to deprotonate O2 this causes the ring to open.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| His270(269)A | metal ligand |
| Asp334(333)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp302(301)A | metal ligand |
| His294(293)A | metal ligand |
| Asp267(266)A | metal ligand |
| Glu234(233)A | metal ligand |
| Asp334(333)A | proton acceptor |
Chemical Components
proton transfer, decyclisation, overall reactant usedCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp334(333)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp302(301)A | metal ligand |
| His294(293)A | metal ligand |
| His270(269)A | metal ligand |
| Asp267(266)A | metal ligand |
| Glu234(233)A | metal ligand |
| Asp334(333)A | proton donor |
Chemical Components
proton transfer
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His270(269)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand |
| Trp193(192)A | activator |
| Lys236(235)A | activator |
| His270(269)A | activator |
| Asp304(303)A | proton acceptor |
Chemical Components
proton transfer, assisted keto-enol tautomerisation
Step 4. A proton is transferred from O2 to O1 via a water molecule and the enolate collapses into the product.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu234(233)A | metal ligand |
| Asp267(266)A | metal ligand |
| His270(269)A | metal ligand |
| His294(293)A | metal ligand |
| Asp302(301)A | metal ligand |
| Asp304(303)A | metal ligand |
| Asp334(333)A | metal ligand |
| Trp193(192)A | activator |
| Lys236(235)A | activator |
| His270(269)A | activator |
| Asp304(303)A | proton donor |
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