spacer
spacer

PDBsum entry 2c3v

Go to PDB code: 
protein metals Protein-protein interface(s) links
Carbohydrate-binding module PDB id
2c3v
Jmol
Contents
Protein chains
94 a.a. *
94 a.a. *
Metals
IOD ×3
Waters ×212
* Residue conservation analysis
PDB id:
2c3v
Name: Carbohydrate-binding module
Title: Structure of iodinated cbm25 from bacillus halodurans amylase
Structure: Alpha-amylase g-6. Chain: a. Fragment: carbohydrate-binding module, residues 863-958. Synonym: family 25 carbohydrate-binding module. Engineered: yes. Alpha-amylase g-6. Chain: b. Fragment: carbohydrate-binding module, residues 863-958. Synonym: family 25 carbohydrate-binding module.
Source: Bacillus halodurans. Organism_taxid: 272558. Strain: c-125. Atcc: baa-125. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.39Å     R-factor:   0.204     R-free:   0.250
Authors: A.B.Boraston,M.Healey,J.Klassen,E.Ficko-Blean, A.Lammerts Van Bueren,V.Law
Key ref:
A.B.Boraston et al. (2006). A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem, 281, 587-598. PubMed id: 16230347 DOI: 10.1074/jbc.M509958200
Date:
12-Oct-05     Release date:   17-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9KFR4  (Q9KFR4_BACHD) -  Alpha-amylase G-6
Seq:
Struc:
 
Seq:
Struc:
958 a.a.
94 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9KFR4  (Q9KFR4_BACHD) -  Alpha-amylase G-6
Seq:
Struc:
 
Seq:
Struc:
958 a.a.
94 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     starch binding     1 term  

 

 
DOI no: 10.1074/jbc.M509958200 J Biol Chem 281:587-598 (2006)
PubMed id: 16230347  
 
 
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, V.Law.
 
  ABSTRACT  
 
Starch-hydrolyzing enzymes lacking alpha-glucan-specific carbohydrate-binding modules (CBMs) typically have lowered activity on granular starch relative to their counterparts with CBMs. Thus, consideration of starch recognition by CBMs is a key factor in understanding granular starch hydrolysis. To this end, we have dissected the modular structure of the maltohexaose-forming amylase from Bacillus halodurans (C-125). This five-module protein comprises an N-terminal family 13 catalytic module followed in order by two modules of unknown function, a family 26 CBM (BhCBM26), and a family 25 CBM (BhCBM25). Here we present a comprehensive structure-function analysis of starch and alpha-glucooligosaccharide recognition by BhCBM25 and BhCBM26 using UV methods, isothermal titration calorimetry, and x-ray crystallography. The results reveal that the two CBMs bind alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, with different affinities but have similar abilities to bind granular starch. Notably, these CBMs appear to recognize the same binding sites in granular starch. The enhanced affinity of the tandem CBMs for granular starch is suggested to be the main biological advantage for this enzyme to contain two CBMs. Structural studies of the native and ligand-bound forms of BhCBM25 and BhCBM26 show a structurally conserved mode of ligand recognition but through non-sequence-conserved residues. Comparison of these CBM structures with other starch-specific CBM structures reveals a generally conserved mode of starch recognition.
 
  Selected figure(s)  
 
Figure 5.
FIGURE 5. Phasing and structures of BhCBM25 and BhCBM26. A, anomalous difference peaks (red) and representative electron density (blue; 0.39 electrons/Å3) contoured around the iodotyrosine heavy atom sites used for SAD phasing of BhCBM25. B, anomalous difference peaks (red) and representative electron density (blue; 0.37 electrons/Å3) contoured around the cadmium sites used for SAD phasing of BhCBM26. C, the overall secondary structure of BhCBM25 as representative of the fold and topology of both BhCBM25 and BhCBM26. Selected amino acid side chains are shown in a "licorice" representation. Electron density maps are maximum likelihood (29)/ [A] (44) weighted 2F[o] - F[c] electron density maps.
Figure 6.
FIGURE 6. Observed electron density for maltotetraose bound to BhCBM25 in the P2[1] crystal form (A), maltotetraose bound to BhCBM25 in the P4[3]2[1]2 crystal form (symmetry-related molecules are colored blue and green) (B), and maltose bound to BhCBM26 (C). The mobile binding loop of BhCBM26 discussed throughout is shown in violet. Relevant amino acid side chains are shown in a "licorice" representation and labeled. All maps are maximum likelihood (29)/ [A] (44) weighted 2F[o] - F[c] electron density maps contoured at 1 (0.30, 0.15, and 0.14 electrons/Å3 in A, B, and C, respectively).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 587-598) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21294843 M.A.Glaring, M.J.Baumann, M.Abou Hachem, H.Nakai, N.Nakai, D.Santelia, B.W.Sigurskjold, S.C.Zeeman, A.Blennow, and B.Svensson (2011).
Starch-binding domains in the CBM45 family--low-affinity domains from glucan, water dikinase and α-amylase involved in plastidial starch metabolism.
  FEBS J, 278, 1175-1185.  
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19052787 R.Rodríguez-Sanoja, N.Oviedo, L.Escalante, B.Ruiz, and S.Sánchez (2009).
A single residue mutation abolishes attachment of the CBM26 starch-binding domain from Lactobacillus amylovorus alpha-amylase.
  J Ind Microbiol Biotechnol, 36, 341-346.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
17187076 A.L.van Bueren, M.Higgins, D.Wang, R.D.Burke, and A.B.Boraston (2007).
Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors.
  Nat Struct Mol Biol, 14, 76-84.
PDB codes: 2j43 2j44
17468268 D.Guillén, M.Santiago, L.Linares, R.Pérez, J.Morlon, B.Ruiz, S.Sánchez, and R.Rodríguez-Sanoja (2007).
Alpha-amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains.
  Appl Environ Microbiol, 73, 3833-3837.  
17090949 H.Watanabe, T.Nishimoto, M.Kubota, H.Chaen, and S.Fukuda (2006).
Cloning, sequencing, and expression of the genes encoding an isocyclomaltooligosaccharide glucanotransferase and an alpha-amylase from a Bacillus circulans strain.
  Biosci Biotechnol Biochem, 70, 2690-2702.  
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.