4EIB | pdb_00004eib

Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight into the Altered Selectivity on Carbohydrate Binding.

PDB DOI: https://doi.org/10.2210/pdb4EIB/pdb

Classification: HYDROLASE
Organism(s): Rhizopus arrhizus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-05 Released: 2012-12-12
Deposition Author(s): Stephen, P., Cheng, K.C., Lyu, P.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites

Stephen, P., Cheng, K.C., Lyu, P.C.

(2012) PLoS One 7: e50488-e50488

PubMed: 23226294 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0050488
Primary Citation Related Structures:
4EIB

PubMed Abstract:
Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates. For the study reported herein, we used a standard soluble ligand (amylose EX-I) to characterize the functional and structural aspects of circularly permuted RoCBM21 (CP90). Site-directed mutagenesis and the analysis of crystal structure reveal the dimerisation and an altered binding path, which may be responsible for improved affinity and altered selectivity of this newly created starch-binding domain. The functional and structural characterization of CP90 suggests that it has significant potential in industrial applications.

Organizational Affiliation

Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.

Macromolecule Content

Total Structure Weight: 25.46 kDa
Atom Count: 1,852
Modeled Residue Count: 216
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucoamylase	A, B	109	Rhizopus arrhizus	Mutation(s): 0 Gene Names: amyA, CBM21 EC: 3.2.1.3
UniProt
Find proteins for B7XC04 (Rhizopus oryzae) Explore B7XC04 Go to UniProtKB: B7XC04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7XC04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B]	C [auth A] D [auth A] F [auth A] R [auth B] S [auth B] C [auth A], D [auth A], F [auth A], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth B] SDF format, chain EA [auth B] SDF format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain CA [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], M [auth A], N [auth A], O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain AA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth B]	AA [auth B] G [auth A] H [auth A] I [auth A] J [auth A] AA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] 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 V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] 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 V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain U [auth B] SDF format, chain HA [auth B] SDF format, chain E [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain U [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain E [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain U [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain E [auth A]	E [auth A], HA [auth B], IA [auth B], U [auth B]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.945	α = 90
b = 66.945	β = 90
c = 44.356	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Stephen, P.

Cheng, K.C.

Lyu, P.C.

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2013-07-24
Changes: Database references
Version 1.2: 2017-08-23
Changes: Refinement description, Source and taxonomy
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description