Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank

Abstract

Taking advantage of the known planarity of the N‐acetyl group of N‐acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N‐acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 Å determined between 2000 and 2015. Though the automated PDB‐REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N‐acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 Å, it produces N‐acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real‐space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.

Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

“…Similar to in a peptide, the bond between N2 and C7 has a bond order higher than 1. As a result, the atoms in the plane can take on a cis - and a trans -conformation with a strong preference for the latter [ 45 ]. The possibility of having two conformations is described in several ways: AceDRG splits the plane into 2 sections and defines the N2-C7 bond as rotatable with target values at 0° and 180°.…”

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…Unfortunately, most of the data obtained on the basis of crystallographic experiments can dramatically differ from glycan conformations in solution or have poor resolution which needs further adjustment [ 299 , 300 ]. Moreover, not all of the objects of interest can be obtained as a single crystal.…”

“…Another issue of concern related to Protein Data Bank is large proportion of errors in deposited coordinates, leading to requirement for a thorough checkup and development of data remediation services [ 319 ]. Commonly occurring problems associated with nomenclature, poor glycan geometry, linkage errors, missing or surplus atoms can seriously decline the quality of the obtained 3D structures [ 300 , 320 , 321 ]. Using Privateer software, it was discovered [ 299 ],[ 301 ] that PDB deposits significant number of erroneous N-glycosylated structures with pyranose ring distortions, considering preferred adoption of 4 C 1 conformation for D-sugars and 1 C 4 conformation for L-sugars ( Figure 9 ).…”

Determination of Amide cis/trans Isomers in N‐Acetyl‐d‐glucosamine: Tailored NMR Analysis of the N‐Acetyl Group Conformation

“…Prior studies show that the amide bond in GlcNAc is predominantly in the trans conformation (the relative orientation of C2 and C2', see Scheme 2), with only about 1.8 % in the cis conformation at 42 °C. [9] However, surveys on glycoprotein X-ray crystal structures found that as much as 6-12 % of the GlcNAc residues populate the cis conformation, [9,15] although a substantial amount of these structures are severely twisted or may be due to an erroneous interchange of the carbonyl oxygen and the methyl carbon, which indicates an overestimation of the amount of cis conformations. [15,16] Thus the amide cis conformation may play an important role in certain glycoconjugates, although characterization of the cis form in monomeric GlcNAc remains challenging due to the low abundance in aqueous solution.…”

“…[9] In this study, the amide protons of the GlcNAc cis forms were observed for the first time and amide protons of both cis and trans forms were investigated by NMR spectroscopy. A series of NMR experiments were utilized to measure J-couplings within the N-acetyl group of uniformly 13 C, 15 N-labeled GlcNAc. 13 C, 15 N-labeling enabled the measurement of eight vicinal scalar coupling constants (one 3 J HH , three 3 J CC , and four 3 J CH ) within the N-acetyl group, of which six are sensitive to the θ 1 angle and two are sensitive to the θ 2 angle (Scheme 1).…”