3REN

CPF_2247, a novel alpha-amylase from Clostridium perfringens

PDB DOI: https://doi.org/10.2210/pdb3REN/pdb

Classification: HYDROLASE
Organism(s): Clostridium perfringens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-04 Released: 2011-05-18
Deposition Author(s): Ficko-Blean, E., Stuart, C.P., Boraston, A.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224
R-Value Work: 0.169
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of CPF_2247, a novel alpha-amylase from Clostridium perfringens.

Ficko-Blean, E., Stuart, C.P., Boraston, A.B.

(2011) Proteins 79: 2771-2777

PubMed: 21905105 Search on PubMed
DOI: https://doi.org/10.1002/prot.23116

PubMed Abstract:
CPF_2247 from Clostridium perfringens ATCC 13124 was identified as a putative carbohydrate-active enzyme by its low sequence identity to endo-β-1,4-glucanases belonging to family 8 of the glycoside hydrolase classification. The X-ray crystal structure of CPF_2247 determined to 2.0 Å resolution by single-wavelength anomalous dispersion using seleno-methionine-substituted protein revealed an (α/α)(6) barrel fold. A large cleft on the surface of the protein contains residues that are structurally conserved with key elements of the catalytic machinery in clan GH-M glycoside hydrolases. Assessment of CPF_2247 as a carbohydrate-active enzyme disclosed α-glucanase activity on amylose, glycogen, and malto-oligosaccharides.

Organizational Affiliation

Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada.

Macromolecule Content

Total Structure Weight: 82.3 kDa
Atom Count: 6,107
Modelled Residue Count: 669
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase, family 8	A, B	350	Clostridium perfringens	Mutation(s): 0 Gene Names: CPF_2247
UniProt
Find proteins for A0A0H2YP60 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YP60 Go to UniProtKB: A0A0H2YP60
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YP60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	E [auth A], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B]	C [auth A], D [auth A], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B]