4GJI

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose

PDB DOI: https://doi.org/10.2210/pdb4GJI/pdb

Classification: ISOMERASE
Organism(s): Stutzerimonas stutzeri
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-08-09 Released: 2012-12-12
Deposition Author(s): Yoshida, H., Kamitori, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.175
R-Value Observed: 0.175

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.

Yoshida, H., Yoshihara, A., Teraoka, M., Yamashita, S., Izumori, K., Kamitori, S.

(2013) FEBS Open Bio 3: 35-40

PubMed: 23772372 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.fob.2012.11.008
Primary Citation of Related Structures:
4GJI, 4GJJ

PubMed Abstract:
l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. To elucidate this mechanism, we determined X-ray structures of a mutant l-RhI in complex with l-rhamnopyranose and d-allopyranose. Results suggest that a catalytic water molecule, which acts as an acid/base catalyst in the isomerization reaction, is likely to be involved in pyranose-ring opening, and that a newly found substrate sub-binding site in the vicinity of the catalytic site may recognize different anomers of substrates.

Organizational Affiliation

Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Macromolecule Content

Total Structure Weight: 194.28 kDa
Atom Count: 15,195
Modelled Residue Count: 1,688
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-rhamnose isomerase	A, B, C, D	438	Stutzerimonas stutzeri	Mutation(s): 2 Gene Names: L-RhI EC: 5.3.1.14
UniProt
Find proteins for Q75WH8 (Stutzerimonas stutzeri) Explore Q75WH8 Go to UniProtKB: Q75WH8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q75WH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RNS Query on RNS Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain E [auth A] SDF format, chain U [auth D] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain U [auth D] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain U [auth D]	E [auth A], J [auth B], O [auth C], U [auth D]	L-RHAMNOSE C₆ H₁₂ O₅ PNNNRSAQSRJVSB-BXKVDMCESA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
RM4 Query on RM4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D]	I [auth B], L [auth B], T [auth D]	beta-L-rhamnopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-YJRYQGEOSA-N		Interactions Focus chain I [auth B] Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth B] Focus chain T [auth D]
RAM Query on RAM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D]	F [auth A], K [auth B], P [auth C], V [auth D]	alpha-L-rhamnopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-HGVZOGFYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	G [auth A] H [auth A] M [auth B] N [auth B] Q [auth C] G [auth A], H [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.175
R-Value Observed: 0.175
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.124	α = 90
b = 104.917	β = 106.01
c = 112.376	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Yoshida, H.

Kamitori, S.

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2014-05-28
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4GJI

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose

Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)