PDBsum entry 8bit

Ligase

PDB id: 8bit

Contents

Protein chains

562 a.a.

Ligands

6R9 ×2

COA ×2

PDB id:

8bit

Name:

Ligase

Title:

Crystal structure of acyl-coa synthetase from metallosphaera sedula in complex with coenzyme a and acetyl-amp

Structure:

4-hydroxybutyrate--coa ligase 1. Chain: b, a. Synonym: acetate--coa ligase,butyrate--coa ligase,propionate--coa ligase. Ec: 6.2.1.40,6.2.1.1,6.2.1.2,6.2.1.17. Engineered: yes

Source:

Metallosphaera sedula dsm 5348. Organism_taxid: 399549. Strain: atcc 51363 / dsm 5348 / jcm 9185 / nbrc 15509 / th2. Gene: msed_0406. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

3.10Å R-factor: 0.214 R-free: 0.277

Authors:

N.Capra,A.M.W.H.Thunnissen,D.B.Janssen

Key ref:

N.Capra et al. Crystal structure of acyl-Coa synthetase from metallo sedula in complex with acetyl-Amp. To be published, .

Date:

02-Nov-22 Release date: 15-Nov-23

Protein chains

A4YDT1  (HBCL1_METS5) -  4-hydroxybutyrate--CoA ligase 1 from Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2)

Seq: 564 a.a.

Struc: 562 a.a.

Enzyme reactions

• Enzyme class 2: E.C.6.2.1.1 - acetate--CoA ligase.
• Reaction: acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate

acetate + ATP + CoA (Bound ligand (Het Group name = COA) corresponds exactly) = acetyl-CoA + AMP (Bound ligand (Het Group name = 6R9) matches with 88.46% similarity) + diphosphate

• Enzyme class 3: E.C.6.2.1.17 - propionate--CoA ligase.
• Reaction: propanoate + ATP + CoA = propanoyl-CoA + AMP + diphosphate

propanoate + ATP (Bound ligand (Het Group name = COA) corresponds exactly) + CoA = propanoyl-CoA (Bound ligand (Het Group name = 6R9) matches with 88.46% similarity) + AMP + diphosphate

• Enzyme class 4: E.C.6.2.1.2 - medium-chain acyl-CoA ligase.
• Reaction: a medium-chain fatty acid + ATP + CoA = a medium-chain fatty acyl-CoA + AMP + diphosphate

medium-chain fatty acid + ATP + CoA (Bound ligand (Het Group name = COA) corresponds exactly) = medium-chain fatty acyl-CoA + AMP (Bound ligand (Het Group name = 6R9) matches with 88.46% similarity) + diphosphate

• Enzyme class 5: E.C.6.2.1.40 - 4-hydroxybutyrate--CoA ligase (AMP-forming).
• Reaction: 4-hydroxybutanoate + ATP + CoA = 4-hydroxybutanoyl-CoA + AMP + diphosphate

4-hydroxybutanoate + ATP + CoA (Bound ligand (Het Group name = COA) corresponds exactly) = 4-hydroxybutanoyl-CoA + AMP (Bound ligand (Het Group name = 6R9) matches with 88.46% similarity) + diphosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site