6J34

Crystal Structure of maltotriose-complex of PulA from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6J34/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-01-09 Released: 2019-09-18
Deposition Author(s): Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.161
R-Value Work: 0.130
R-Value Observed: 0.132

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase.

Saka, N., Malle, D., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.

(2019) Acta Crystallogr D Struct Biol 75: 792-803

PubMed: 31478902 Search on PubMed
DOI: https://doi.org/10.1107/S2059798319010660
Primary Citation of Related Structures:
6J33, 6J34, 6J35, 6J4H

PubMed Abstract:
Klebsiella pneumoniae pullulanase (KPP) belongs to glycoside hydrolase family 13 subfamily 13 (GH13_13) and is the only enzyme that is reported to perform an induced-fit motion of the active-site loop (residues 706-710). Comparison of pullulanase structures indicated that only KPP has Leu680 present behind the loop, in contrast to the glycine found in other GH13_13 members. Analysis of the structure and activity of recombinant pullulanase from K. pneumoniae ATCC 9621 (rKPP) and its mutant (rKPP-G680L) indicated that the side chain of residue 680 is important for the induced-fit motion of the loop 706-710 and alters the binding affinity of the substrate.

Organizational Affiliation

Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

Macromolecule Content

Total Structure Weight: 116 kDa
Atom Count: 8,686
Modelled Residue Count: 930
Deposited Residue Count: 1,053
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pullulanase	A	1,053	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: pulA EC: 3.2.1.41
UniProt
Find proteins for W9BQ28 (Klebsiella pneumoniae) Explore W9BQ28 Go to UniProtKB: W9BQ28
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W9BQ28
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B, C	3		N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [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] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009 Query on PRD_900009	B, C	alpha-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.161
R-Value Work: 0.130
R-Value Observed: 0.132
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.891	α = 90
b = 60.119	β = 114.69
c = 133.829	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
HKL-2000	data collection

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP16H04909

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary