1CBU

ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM

Summary for 1CBU

• Entry DOI: 10.2210/pdb1cbu/pdb
• Descriptor: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE, SULFATE ION (3 entities in total)
• Functional Keywords: cobalamin biosynthesis, adenosylcobinamide, kinase, atpase, guanylyltransferase, salmonella typhimurium, transferase, coenzyme b12
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 3
• Total formula weight: 59672.32

Authors

Thompson, T.B.,Thomas, M.G.,Escalante-Semerena, J.C.,Rayment, I. (deposition date: 1998-03-12, release date: 1998-12-02, Last modification date: 2024-02-07)

Primary citation

Thompson, T.B.,Thomas, M.G.,Escalante-Semerena, J.C.,Rayment, I.
Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,.
Biochemistry, 37:7686-7695, 1998

PubMed Abstract: The X-ray structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) from Salmonella typhimurium has been determined to 2.3 A resolution. This enzyme of subunit molecular weight 19 770 plays a central role in the assembly of the nucleotide loop for adenosylcobalamin where it catalyzes both the phosphorylation of the 1-amino-2-propanol side chain of the corrin ring and the subsequent attachment of GMP to form the product adenosylcobinamide-GDP. The kinase activity is believed to be associated with a P-loop motif, whereas the transferase activity proceeds at a different site on the enzyme via a guanylyl intermediate. The enzyme was crystallized in the space group C2221 with unit cell dimensions of a = 96.4 A, b = 114.4 A, and c = 106.7 A, with three subunits per asymmetric unit. The structure reveals that the enzyme is a molecular trimer and appears somewhat like a propeller with overall molecular dimensions of approximately 64 A x 77 A x 131 A. Each subunit consists of a single domain that is dominated by a seven-stranded mixed beta-sheet flanked on either side by a total of five alpha-helices and one helical turn. Six of the seven beta-strands run parallel. The C-terminal strand lies at the edge of the sheet and runs antiparallel to the others. Interestingly, CobU displays a remarkable structural and topological similarity to the central domain of the RecA protein, although the reason for this observation is unclear. The structure contains a P-loop motif located at the base of a prominent cleft formed by the association of two subunits and is most likely the kinase active site. Each subunit of CobU contains a cis peptide bond between Glu80 and Cys81 where Glu80 faces the P-loop and might serve to coordinate the magnesium ion of the triphosphate substrate. Interestingly, His46, which is the putative site for guanylylation, lies approximately 21 A from the P-loop and is solvent-exposed. This suggests that the enzyme undergoes a conformational change when the substrates bind to bring these two active sites into closer proximity.

PubMed: 9601028
DOI: 10.1021/bi973178f

Experimental method

X-RAY DIFFRACTION (2.3 Å)