4DDN

Structure analysis of a wound-inducible lectin ipomoelin from sweet potato

PDB DOI: https://doi.org/10.2210/pdb4DDN/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ipomoea batatas
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-19 Released: 2012-08-01
Deposition Author(s): Chang, W.C., Liu, K.L., Jeng, S.T., Hsu, F.C., Cheng, Y.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.186

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Ipomoelin, a jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus.

Chang, W.C., Liu, K.L., Hsu, F.C., Jeng, S.T., Cheng, Y.S.

(2012) PLoS One 7: e40618-e40618

PubMed: 22808208 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0040618
Primary Citation of Related Structures:
3R50, 3R51, 3R52, 4DDN

PubMed Abstract:
Many proteins are induced in the plant defense response to biotic stress or mechanical wounding. One group is lectins. Ipomoelin (IPO) is one of the wound-inducible proteins of sweet potato (Ipomoea batatas cv. Tainung 57) and is a Jacalin-related lectin (JRL). In this study, we resolved the crystal structures of IPO in its apo form and in complex with carbohydrates such as methyl α-D-mannopyranoside (Me-Man), methyl α-D-glucopyranoside (Me-Glc), and methyl α-D-galactopyranoside (Me-Gal) in different space groups. The packing diagrams indicated that IPO might represent a compact tetrameric association in the JRL family. The protomer of IPO showed a canonical β-prism fold with 12 strands of β-sheets but with 2 additional short β-strands at the N terminus. A truncated IPO (ΔN10IPO) by removing the 2 short β-strands of the N terminus was used to reveal its role in a tetrameric association. Gel filtration chromatography confirmed IPO as a tetrameric form in solution. Isothermal titration calorimetry determined the binding constants (K(A)) of IPO and ΔN10IPO against various carbohydrates. IPO could bind to Me-Man, Me-Glc, and Me-Gal with similar binding constants. In contrast, ΔN10IPO showed high binding ability to Me-Man and Me-Glc but could not bind to Me-Gal. Our structural and functional analysis of IPO revealed that its compact tetrameric association and carbohydrate binding polyspecificity could be regulated by the 2 additional N-terminal β-strands. The versatile carbohydrate binding properties of IPO might play a role in plant defense.

Organizational Affiliation

Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan, Republic of China.

Macromolecule Content

Total Structure Weight: 70.16 kDa
Atom Count: 5,010
Modelled Residue Count: 616
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ipomoelin	A, B, C, D	160	Ipomoea batatas	Mutation(s): 0
UniProt
Find proteins for P93193 (Ipomoea batatas) Explore P93193 Go to UniProtKB: P93193
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P93193
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMG Query on AMG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	methyl alpha-D-galactopyranoside C₇ H₁₄ O₆ HOVAGTYPODGVJG-PZRMXXKTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 82.075	α = 90
b = 83.931	β = 90
c = 86.129	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary