5YSN | pdb_00005ysn

Ethanolamine ammonia-lyase, AdoCbl/substrate-free

PDB DOI: https://doi.org/10.2210/pdb5YSN/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-11-14 Released: 2018-09-19
Deposition Author(s): Shibata, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.192 (Depositor), 0.212 (DCC)
R-Value Work:
0.163 (Depositor), 0.181 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.

Shibata, N., Sueyoshi, Y., Higuchi, Y., Toraya, T.

(2018) Angew Chem Int Ed Engl 57: 7830-7835

PubMed: 29797764 Search on PubMed
DOI: https://doi.org/10.1002/anie.201803591
Primary Citation Related Structures:
5YRT, 5YRV, 5YSH, 5YSN, 5YSR

PubMed Abstract:
The crystal structures of the B ₁₂ -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.

Organizational Affiliation

Department of Picobiology/Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.

Macromolecule Content

Total Structure Weight: 166.71 kDa
Atom Count: 12,142
Modeled Residue Count: 1,410
Deposited Residue Count: 1,496
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine ammonia-lyase heavy chain	A, C	453	Escherichia coli K-12	Mutation(s): 0 Gene Names: eutB, b2441, JW2434 EC: 4.3.1.7
UniProt
Find proteins for P0AEJ6 (Escherichia coli (strain K12)) Explore P0AEJ6 Go to UniProtKB: P0AEJ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEJ6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine ammonia-lyase light chain	B, D	295	Escherichia coli K-12	Mutation(s): 0 Gene Names: eutC, b2440, JW2433 EC: 4.3.1.7
UniProt
Find proteins for P19636 (Escherichia coli (strain K12)) Explore P19636 Go to UniProtKB: P19636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain S [auth D] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D]	L [auth B], S [auth D]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain L [auth B] Focus chain S [auth D] Interactions & Density Focus chain L [auth B] Focus chain S [auth D]
5AD Query on 5AD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
GOL Query on GOL 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 K [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] 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 K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] 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 K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain J [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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] Focus chain K [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] 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] Focus chain K [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]