3LBF | pdb_00003lbf

Crystal structure of Protein L-isoaspartyl methyltransferase from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3LBF/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-08 Released: 2010-09-08
Deposition Author(s): Fang, P., Li, X., Wang, J., Niu, L., Teng, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.247 (Depositor), 0.251 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the protein L-isoaspartyl methyltransferase from Escherichia coli

Fang, P., Li, X., Wang, J., Xing, L., Gao, Y., Niu, L., Teng, M.

(2010) Cell Biochem Biophys 58: 163-167

PubMed: 20857228 Search on PubMed
DOI: https://doi.org/10.1007/s12013-010-9103-2
Primary Citation Related Structures:
3LBF

PubMed Abstract:
Among the known covalent damages that can occur spontaneously to proteins, the formation of isoaspartyl linkages through deamidation of asparagines and isomerization of aspartates may be one of the most rapid forms under conditions of physiological pH and temperature. The protein L-isoaspartyl methyltransferase (PIMT) is thought to recognize L-isoaspartyl residues and repair this kind of damaged proteins. Curiously, there is a potential functional difference between bacterial and mammalian PIMTs. Herein, we present the crystal structure of Escherichia coli PIMT (EcPIMT) at a resolution of 1.8 Å. The enzyme we investigated was able to remain bound to its product S-adenosylhomocysteine (SAH) during crystallization. Analysis indicates that the high affinity of EcPIMT for SAH might lead to the lower activity of the enzyme.

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, People's Republic of China.

Macromolecule Content

Total Structure Weight: 96.14 kDa
Atom Count: 6,657
Modeled Residue Count: 817
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-L-isoaspartate O-methyltransferase	A, B, C, D	210	Escherichia coli K-12	Mutation(s): 0 EC: 2.1.1.77
UniProt
Find proteins for P0A7A5 (Escherichia coli (strain K12)) Explore P0A7A5 Go to UniProtKB: P0A7A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7A5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C], O [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], N [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.247 (Depositor), 0.251 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.3	α = 74
b = 55.06	β = 74.7
c = 67.49	γ = 85.57

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-03-05
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description