7C11 | pdb_00007c11

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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(2020) Biochem Biophys Res Commun 528: 426-431

PubMed Abstract:
Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that K _m value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.

Organizational Affiliation

School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate-tetrahydrofolate ligase	A B C D E [auth M] A, B, C, D, E [auth M], F [auth N], G [auth O], H [auth P]	568	Methylorubrum extorquens CM4	Mutation(s): 0 Gene Names: fhs, Mchl_0447 EC: 6.3.4.3
UniProt
Find proteins for B7L0A5 (Methylorubrum extorquens (strain CM4 / NCIMB 13688)) Explore B7L0A5 Go to UniProtKB: B7L0A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7L0A5
Sequence Annotations Expand
Reference Sequence

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain K [auth N] MOL2 format, chain K [auth N] mmCIF format, chain K [auth N]	K [auth N]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain K [auth N] Interactions & Density Focus chain K [auth N]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]