spacer
spacer

PDBsum entry 1de6

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1de6
Jmol
Contents
Protein chains
416 a.a. *
Ligands
RNS ×4
Metals
_MN ×4
_ZN ×4
Waters ×1043
* Residue conservation analysis
PDB id:
1de6
Name: Isomerase
Title: L-rhamnose isomerase
Structure: L-rhamnose isomerase. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: pik61.
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.173     R-free:   0.244
Authors: I.P.Korndorfer,W.D.Fessner,B.W.Matthews
Key ref:
I.P.Korndörfer et al. (2000). 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. J Mol Biol, 300, 917-933. PubMed id: 10891278 DOI: 10.1006/jmbi.2000.3896
Date:
13-Nov-99     Release date:   09-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P32170  (RHAA_ECOLI) -  L-rhamnose isomerase
Seq:
Struc:
419 a.a.
416 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.14  - L-rhamnose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-rhamnopyranose = L-rhamnulose
L-rhamnopyranose
Bound ligand (Het Group name = RNS)
corresponds exactly
= L-rhamnulose
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     rhamnose metabolic process   3 terms 
  Biochemical function     isomerase activity     4 terms  

 

 
    Key reference    
 
 
DOI no: 10.1006/jmbi.2000.3896 J Mol Biol 300:917-933 (2000)
PubMed id: 10891278  
 
 
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.
I.P.Korndörfer, W.D.Fessner, B.W.Matthews.
 
  ABSTRACT  
 
Using a new expression construct, rhamnose isomerase from Escherichia coli was purified and crystallized. The crystal structure was solved by multiple isomorphous replacement and refined to a crystallographic residual of 17.4 % at 1.6 A resolution. Rhamnose isomerase is a tight tetramer of four (beta/alpha)(8)-barrels. A comparison with other known structures reveals that rhamnose isomerase is most similar to xylose isomerase. Alignment of the sequences of the two enzymes based on their structures reveals a hitherto undetected sequence identity of 13 %, suggesting that the two enzymes evolved from a common precursor. The structure and arrangement of the (beta/alpha)(8)-barrels of rhamnose isomerase are very similar to xylose isomerase. Each enzyme does, however, have additional alpha-helical domains, which are involved in tetramer association, and largely differ in structure. The structures of complexes of rhamnose isomerase with the inhibitor l-rhamnitol and the natural substrate l-rhamnose were determined and suggest that an extended loop, which is disordered in the native enzyme, becomes ordered on substrate binding, and may exclude bulk solvent during catalysis. Unlike xylose isomerase, this loop does not extend across a subunit interface but contributes to the active site of its own subunit. It illustrates how an interconversion between inter and intra-subunit complementation can occur during evolution. In the crystal structure (although not necessarily in vivo) rhamnose isomerase appears to bind Zn(2+) at a "structural" site. In the presence of substrate the enzyme also binds Mn(2+) at a nearby "catalytic" site. An array of hydrophobic residues, not present in xylose isomerase, is likely to be responsible for the recognition of l-rhamnose as a substrate. The available structural data suggest that a metal-mediated hydride-shift mechanism, which is generally favored for xylose isomerase, is also feasible for rhamnose isomerase.
 
  Selected figure(s)  
 
Figure 11.
Figure 11. Proposed reaction mechanism for rhamnose isomerase. Distances are taken from the complex with rhamnitol assuming the presence of a catalytic water molecule as seen in xylose isomerase.
Figure 12.
Figure 12. Superposition of the structures of rhamnose isomerase and xylose isomerase in the vicinity of a subunit interface showing how the respective active sites are constructed in different ways. The active sites are marked by bound inhibitors, shown in yellow. In rhamnose isomerase the b1-a1-loop (red) of one subunit becomes ordered on inhibitor binding and covers the active site of the same subunit. In xylose isomerase the b1-a1-loop (cyan) of one sub- unit extends across the subunit interface and reaches into the active site of a neighboring subunit.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 917-933) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058398 C.Roux, F.Bhatt, J.Foret, B.de Courcy, N.Gresh, J.P.Piquemal, C.J.Jeffery, and L.Salmon (2011).
The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies.
  Proteins, 79, 203-220.  
20852996 P.Prabhu, T.T.Doan, M.Jeya, L.W.Kang, and J.K.Lee (2011).
Cloning and characterization of a rhamnose isomerase from Bacillus halodurans.
  Appl Microbiol Biotechnol, 89, 635-644.  
20977999 H.Yoshida, K.Takeda, K.Izumori, and S.Kamitori (2010).
Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of pseudomonas stutzeri L-rhamnose isomerase.
  Protein Eng Des Sel, 23, 919-927.
PDB codes: 3m0h 3m0l 3m0m 3m0v 3m0x 3m0y
20088877 H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, and S.Kamitori (2010).
Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures.
  FEBS J, 277, 1045-1057.
PDB codes: 3itl 3ito 3itt 3itv 3itx 3ity 3iud 3iuh 3iui
20037152 S.Hou, L.E.Vigeland, G.Zhang, R.Xu, M.Li, S.H.Heinemann, and T.Hoshi (2010).
Zn2+ activates large conductance Ca2+-activated K+ channel via an intracellular domain.
  J Biol Chem, 285, 6434-6442.  
  18931442 K.Takeda, H.Yoshida, G.Takada, K.Izumori, and S.Kamitori (2008).
Overexpression, purification, crystallization and preliminary X-ray crystal analysis of Bacillus pallidusD-arabinose isomerase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 945-948.  
17653540 W.Poonperm, G.Takata, H.Okada, K.Morimoto, T.B.Granström, and K.Izumori (2007).
Cloning, sequencing, overexpression and characterization of L-rhamnose isomerase from Bacillus pallidus Y25 for rare sugar production.
  Appl Microbiol Biotechnol, 76, 1297-1307.  
  16754978 H.Yoshida, P.Wayoon, G.Takada, K.Izumori, and S.Kamitori (2006).
Crystallization and preliminary X-ray diffraction studies of L-rhamnose isomerase from Pseudomonas stutzeri.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 550-552.  
15576371 S.R.Shouldice, D.E.McRee, D.R.Dougan, L.W.Tari, and A.B.Schryvers (2005).
Novel anion-independent iron coordination by members of a third class of bacterial periplasmic ferric ion-binding proteins.
  J Biol Chem, 280, 5820-5827.
PDB codes: 1xvx 1xvy
15184124 K.Leang, G.Takada, A.Ishimura, M.Okita, and K.Izumori (2004).
Cloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli.
  Appl Environ Microbiol, 70, 3298-3304.  
15060078 K.S.Ryu, C.Kim, I.Kim, S.Yoo, B.S.Choi, and C.Park (2004).
NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration.
  J Biol Chem, 279, 25544-25548.  
12595702 C.Davies, and H.Muirhead (2003).
Structure of native phosphoglucose isomerase from rabbit: conformational changes associated with catalytic function.
  Acta Crystallogr D Biol Crystallogr, 59, 453-465.
PDB code: 1n8t
11910031 I.P.Korndörfer, and A.Skerra (2002).
Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site.
  Protein Sci, 11, 883-893.
PDB codes: 1kff 1kl3 1kl4 1kl5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.