PDBsum entry 4r9u

Hydrolase

PDB id: 4r9u

Contents

Protein chains

324 a.a.

248 a.a.

Ligands

LDA ×4

ANP ×2

Metals

_MG ×2

PDB id:

4r9u

Name:

Hydrolase

Title:

Structure of vitamin b12 transporter btucd in a nucleotide-bound outward facing state

Structure:

Vitamin b12 import system permease protein btuc. Chain: a, b. Engineered: yes. Mutation: yes. Vitamin b12 import atp-binding protein btud. Chain: c, d. Synonym: vitamin b12-transporting atpase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: btuc, b1711, jw1701. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: btud, b1709, jw1699. Expression_system_taxid: 562

Resolution:

2.79Å R-factor: 0.218 R-free: 0.247

Authors:

V.M.Korkhov,S.A.Mireku,D.B.Veprintsev,K.P.Locher

Key ref:

V.M.Korkhov et al. (2014). Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F. Nat Struct Biol, 21, 1097-1099. PubMed id: 25402482 DOI: 10.1038/nsmb.2918

Date:

08-Sep-14 Release date: 19-Nov-14

Protein chains

P06609  (BTUC_ECOLI) -  Vitamin B12 import system permease protein BtuC from Escherichia coli (strain K12)

Seq: 326 a.a.

Struc: 324 a.a.*

Protein chains

P06611  (BTUD_ECOLI) -  Vitamin B12 import ATP-binding protein BtuD from Escherichia coli (strain K12)

Seq: 249 a.a.

Struc: 248 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.3.6.3.33 - Transferred entry: 7.6.2.8.
• Reaction: ATP + H₂O + vitamin B12(Out) = ADP + phosphate + vitamin B12(In)

ATP + H(2)O + vitamin B12(Out) = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + vitamin B12(In)

• Enzyme class 3: Chains C, D: E.C.7.6.2.8 - ABC-type vitamin B12 transporter.
• Reaction: an R-cob(III)alamin(out) + ATP + H2O = an R-cob(III)alamin(in) + ADP + phosphate + H⁺

R-cob(III)alamin(out) + ATP + H2O = R-cob(III)alamin(in) (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + phosphate + H(+)

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

reference

DOI no: 10.1038/nsmb.2918

Nat Struct Biol 21:1097-1099 (2014)

PubMed id: 25402482

Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F.

V.M.Korkhov, S.A.Mireku, D.B.Veprintsev, K.P.Locher.

ABSTRACT

The reaction mechanism of BtuCD-F-catalyzed vitamin B12 transport into Escherichia coli is currently unclear. Here we present the structure of the last missing state in the form of AMP-PNP-bound BtuCD, trapped by a disulfide cross-link. Our structural and biochemical data allow a consistent mechanism to be formulated, thus rationalizing the roles of substrate, ATP and substrate-binding protein.