PDBsum entry 4fdv

Isomerase

PDB id: 4fdv

Contents

Protein chain

208 a.a.

Ligands

0UK

GOL ×2

Waters ×224

PDB id:

4fdv

Name:

Isomerase

Title:

Cobh from rhodobacter capsulatus (sb1003) in complex with hba

Structure:

Precorrin-8x methylmutase. Chain: a. Engineered: yes

Source:

Rhodobacter capsulatus. Organism_taxid: 272942. Strain: atcc baa-309 / nbrc 16581 / sb1003. Gene: cobh, rcap_rcc02046. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.68Å R-factor: 0.167 R-free: 0.200

Authors:

R.W.Pickersgill,S.Schroeder,E.Deery,M.J.Warren

Key ref:

E.Deery et al. (2012). An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nat Chem Biol, 8, 933-940. PubMed id: 23042036

Date:

29-May-12 Release date: 17-Oct-12

Protein chain

D5AV08  (D5AV08_RHOCB) -  Precorrin-8X methylmutase from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

Seq: 209 a.a.

Struc: 208 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.1.2 - Transferred entry: 5.4.99.61.
• Pathway: Corrin Biosynthesis (part 4)
• Reaction: Precorrin-8X = hydrogenobyrinate

Precorrin-8X = hydrogenobyrinate (Bound ligand (Het Group name = 0UK) corresponds exactly)

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

Added reference

Nat Chem Biol 8:933-940 (2012)

PubMed id: 23042036

An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.

E.Deery, S.Schroeder, A.D.Lawrence, S.L.Taylor, A.Seyedarabi, J.Waterman, K.S.Wilson, D.Brown, M.A.Geeves, M.J.Howard, R.W.Pickersgill, M.J.Warren.

ABSTRACT

The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.