PDBsum entry: 1pmj

Hydrolase

PDB id: 1pmj

Contents

Protein chain

185 a.a.

Ligands

EDO ×2

ACY

Metals

_CA

Waters ×290

PDB id:

1pmj

Name:

Hydrolase

Title:

Crystal structure of caldicellulosiruptor saccharolyticus cbm27-1

Structure:

Beta-1,4-mannanase. Chain: x. Fragment: carbohydrate-binding module. Synonym: cscbm27-1. Engineered: yes

Source:

Caldicellulosiruptor saccharolyticus. Organism_taxid: 44001. Strain: rt8b.4. Gene: mana. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.128 R-free: 0.174

Authors:

Y.Roske,A.Sunna,U.Heinemann

Key ref:

Y.Roske et al. (2004). High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose. J Mol Biol, 340, 543-554. PubMed id: 15210353 DOI: 10.1016/j.jmb.2004.04.072

Date:

11-Jun-03 Release date: 22-Jun-04

Protein chain

P77847  (P77847_CALSA) -  Beta-1,4-mannanase

Seq: 911 a.a.

Struc: 185 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.78 - Mannan endo-1,4-beta-mannosidase.
• Reaction: Random hydrolysis of 1,4-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.

DOI no: 10.1016/j.jmb.2004.04.072

J Mol Biol 340:543-554 (2004)

PubMed id: 15210353

High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose.

Y.Roske, A.Sunna, W.Pfeil, U.Heinemann.

ABSTRACT

Carbohydrate-binding modules (CBMs) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. Despite the large number of putative CBMs being identified by amino acid sequence alignments, only few representatives have been experimentally shown to have a carbohydrate-binding function. Caldicellulosiruptor strain Rt8B.4 Man26 is a thermostable modular glycoside hydrolase beta-mannanase which contains two non-catalytic modules in tandem at its N terminus. These modules were recently shown to function primarily as beta-mannan-binding modules and have accordingly been classified as members of a novel family of CBMs, family 27. The N-terminal CBM27 (CsCBM27-1) of Man26 from Caldicellulosiruptor Rt8B.4 displays high-binding affinity towards mannohexaose with a Ka of 1 x 10(7) M(-1). Accordingly, the high-resolution crystal structures of CsCBM27-1 native and its mannohexaose complex were solved at 1.55 angstroms and 1.06 angstoms resolution, respectively. In the crystal, CsCBM27-1 shows the typical beta-sandwich jellyroll fold observed in other CBMs with a single metal ion bound, which was identified as calcium. The crystal structures reveal that the overall fold of CsCBM27-1 remains virtually unchanged upon sugar binding and that binding is mediated by three solvent-exposed tryptophan residues and few direct hydrogen bonds. Based on binding affinity and thermal unfolding experiments this structural calcium is shown to play a role in the thermal stability of CsCBM27-1 at high temperatures. The higher binding affinity of CsCBM27-1 to mannooligosaccharides when compared to other members of CBM family 27 might be explained by the different orientation of the residues forming the "aromatic platform" and by differences in the length of loops. Finally, evidence is presented, on the basis of fold similarities and the retention of the position of conserved motifs and a calcium ion, for the consolidation of related CBM families into a superfamily of CBMs.

Selected figure(s)

Figure 3.
Figure 3. Stereo representation of the ligand-binding site of CsCBM27-1. The four b-strands lining the binding cleft are shown in blue. Tryptophan residues forming the aromatic platform that are involved in stacking interactions with the sugar rings of the mannohexaose are depicted in dark blue. The mannohexaose with its alternative conformation for the sixth mannose residue is shown in dark grey and red (oxygen).

Figure 6.
Figure 6. Stereo superposition of the observed conformations of mannohexaose bound to CsCBM27-1 and TmCBM27. The tryptophan residues and mannohexaose are shown in dark blue and yellow in CsCBM27-1 and TmCBM27, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 543-554) copyright 2004.

Figures were selected by an automated process.