6PAE

Dickeya chrysanthemi complex with L-Asp at pH 5.6

PDB DOI: https://doi.org/10.2210/pdb6PAE/pdb

Classification: HYDROLASE
Organism(s): Dickeya chrysanthemi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-11 Released: 2019-09-04
Deposition Author(s): Lubkowski, J., Wlodawer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.176
R-Value Work: 0.137
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.

Lubkowski, J., Wlodawer, A.

(2019) Protein Sci 28: 1850-1864

PubMed: 31423681 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.3709
Primary Citation of Related Structures:
6PA2, 6PA3, 6PA4, 6PA5, 6PA6, 6PA8, 6PA9, 6PAA, 6PAB, 6PAC, 6PAE

PubMed Abstract:
Twenty crystal structures of the complexes of l-asparaginase with l-Asn, l-Asp, and succinic acid that are currently available in the Protein Data Bank, as well as 11 additional structures determined in the course of this project, were analyzed in order to establish the level of conservation of the geometric parameters describing interactions between the substrates and the active site of the enzymes. We found that such stereochemical relationships are highly conserved, regardless of the organism from which the enzyme was isolated, specific crystallization conditions, or the nature of the ligands. Analysis of the geometry of the interactions, including Bürgi-Dunitz and Flippin-Lodge angles, indicated that Thr12 (Escherichia coli asparaginase II numbering) is optimally placed to be the primary nucleophile in the most likely scenario utilizing a double-displacement mechanism, whereas catalysis through a single-displacement mechanism appears to be the least likely.

Organizational Affiliation

Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland.

Macromolecule Content

Total Structure Weight: 141.43 kDa
Atom Count: 11,140
Modelled Residue Count: 1,248
Deposited Residue Count: 1,308
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-asparaginase	A, B, C, D	327	Dickeya chrysanthemi	Mutation(s): 0 Gene Names: ansB, asn EC: 3.5.1.1
UniProt
Find proteins for P06608 (Dickeya chrysanthemi) Explore P06608 Go to UniProtKB: P06608
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06608
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP (Subject of Investigation/LOI) Query on ASP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], K [auth B], L [auth C], N [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
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] 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] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	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] 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]