6PA5

ECAII(T89V,K162T) MUTANT IN COMPLEX WITH L-ASN AT PH 8.3 IN SPACE GROUP P2(1)

PDB DOI: https://doi.org/10.2210/pdb6PA5/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.170
R-Value Observed: 0.171

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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: 287.19 kDa
Atom Count: 21,351
Modelled Residue Count: 2,558
Deposited Residue Count: 2,672
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 2	A, B, C, D, E A, B, C, D, E, F, G, H	334	Escherichia coli K-12	Mutation(s): 2 Gene Names: ansB, b2957, JW2924 EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805 Go to UniProtKB: P00805
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00805
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASN (Subject of Investigation/LOI) Query on ASN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	I [auth A] L [auth B] O [auth C] Q [auth D] T [auth E] I [auth A], L [auth B], O [auth C], Q [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	ASPARAGINE C₄ H₈ N₂ O₃ DCXYFEDJOCDNAF-REOHCLBHSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain S [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D]	K [auth A], N [auth B], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	J [auth A] M [auth B] P [auth C] R [auth D] U [auth E] J [auth A], M [auth B], P [auth C], R [auth D], U [auth E], W [auth F], Y [auth G]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.170
R-Value Observed: 0.171
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.53	α = 90
b = 62.335	β = 117.68
c = 151.047	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-09-04

Deposition Author(s):

Lubkowski, J.

Wlodawer, A.

Revision History (Full details and data files)

Version 1.0: 2019-09-04
Type: Initial release
Version 1.1: 2019-09-25
Changes: Data collection, Database references
Version 1.2: 2019-10-02
Changes: Data collection, Database references
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary

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6PA5

ECAII(T89V,K162T) MUTANT IN COMPLEX WITH L-ASN AT PH 8.3 IN SPACE GROUP P2(1)

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

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)