PDBsum entry 6cbk

Transferase

PDB id: 6cbk

Contents

Protein chains

409 a.a.

Ligands

PMP ×4

EDO

Metals

_NA

Waters ×971

PDB id:

6cbk

Name:

Transferase

Title:

X-ray structure of neob from streptomyces fradiae in complex with pmp

Structure:

Neamine transaminase neon. Chain: a, b, c, d. Synonym: glutamate--6'-dehydroparomamine aminotransferase,neomycin c transaminase,neomycin biosynthesis protein 18,neo-18,neomycin biosynthesis protein b,neomycin biosynthesis protein n. Engineered: yes

Source:

Streptomyces fradiae. Streptomyces roseoflavus. Organism_taxid: 1906. Gene: neon, neo18, neob. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.75Å R-factor: 0.176 R-free: 0.208

Authors:

J.B.Thoden,G.T.Dow,H.M.Holden

Key ref:

G.T.Dow et al. (2018). The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin. Protein Sci, 27, 945-956. PubMed id: 29516565 DOI: 10.1002/pro.3400

Date:

03-Feb-18 Release date: 07-Mar-18

Protein chains

Q53U08  (NEON_STRFR) -  Neamine transaminase NeoN from Streptomyces fradiae

Seq: 416 a.a.

Struc: 409 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.6.1.93 - neamine transaminase.
• Reaction: neamine + 2-oxoglutarate = 6'-oxoparomamine + L-glutamate

neamine (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + 2-oxoglutarate = 6'-oxoparomamine + L-glutamate

• Enzyme class 2: E.C.2.6.1.95 - neomycin C transaminase.
• Reaction: neomycin C + 2-oxoglutarate = 6'''-deamino-6'''-oxoneomycin C + L-glutamate

neomycin C (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + 2-oxoglutarate = 6'''-deamino-6'''-oxoneomycin C + L-glutamate

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: 10.1002/pro.3400

Protein Sci 27:945-956 (2018)

PubMed id: 29516565

The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin.

G.T.Dow, J.B.Thoden, H.M.Holden.

ABSTRACT

The aminoglycoside antibiotics, discovered as natural products in the 1940s, demonstrate a broad antimicrobial spectrum. Due to their nephrotoxic and ototoxic side effects, however, their widespread clinical usage has typically been limited to the treatment of serious infections. Neomycin B, first isolated from strains of Streptomyces in 1948, is one such drug that was approved for human use by the U.S. Food and Drug Administration in 1964. Only within the last 11 years has the biochemical pathway for its production been elaborated, however. Here we present the three-dimensional architecture of NeoB from Streptomyces fradiae, which is a pyridoxal 5'-phosphate or PLP-dependent aminotransferase that functions on two different substrates in neomycin B biosynthesis. For this investigation, four high resolution X-ray structures of NeoB were determined in various complexed states. The overall fold of NeoB is that typically observed for members of the "aspartate aminotransferase" family with the exception of an additional three-stranded antiparallel β-sheet that forms part of the subunit-subunit interface of the dimer. The manner in which the active site of NeoB accommodates quite different substrates has been defined by this investigation. In addition, during the course of this study, we also determined the structure of the aminotransferase GenB1 to high resolution. GenB1 functions as an aminotransferase in gentamicin biosynthesis. Taken together, the structures of NeoB and GenB1, presented here, provide the first detailed descriptions of aminotransferases that specifically function on aldehyde moieties in aminoglycoside biosynthesis.