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Literature summary extracted from

  • Park, J.; Kim, H.; Kim, S.; Lee, D.; Kim, M.S.; Shin, D.H.
    Crystal structure of D-glycero-beta-D-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei (2018), Proteins, 86, 124-131 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.7.70 purified SeMet-labeled and wild-type His6-tagged enzymes are crystallized from 0.1 M HEPES, pH 7.0, 20% w/v PEG 3350, 8.5 mM n-octyl-beta-D-thiomaltoside, and from 0.1 M MES, pH 6.5, 15% w/v PEG 3350, and 6-cyclohexyl-L-hexyl-beta-D-maltoside, respectively, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 2.80 A and 2.40 A resolution, respectively, modeling, the refined model of SeMet-BpHldC is used as a search model for molecular replacement (MR) to solve the structure of native BpHldC Burkholderia pseudomallei

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.7.70 D-glycero-beta-D-manno-heptose 1-phosphate + ATP Burkholderia pseudomallei
-
 ADP-D-glycero-beta-D-manno-heptose + diphosphate
-
 ?
2.7.7.70 D-glycero-beta-D-manno-heptose 1-phosphate + ATP Burkholderia pseudomallei K96243
-
 ADP-D-glycero-beta-D-manno-heptose + diphosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.7.70 Burkholderia pseudomallei Q63XZ4
-
-
2.7.7.70 Burkholderia pseudomallei K96243 Q63XZ4
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.7.70 D-glycero-beta-D-manno-heptose 1-phosphate + ATP
-
 Burkholderia pseudomallei ADP-D-glycero-beta-D-manno-heptose + diphosphate
-
 ?
2.7.7.70 D-glycero-beta-D-manno-heptose 1-phosphate + ATP
-
 Burkholderia pseudomallei K96243 ADP-D-glycero-beta-D-manno-heptose + diphosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.7.70 dimer the wild-type overall architecture belongs to a three layer (alpha/beta/alpha) sandwich structure with a central beta-sheet topology followed by a C-terminal helix through a flexible loop. There are four protomers in the unit cell and all of them exist in a dimeric form. The different contacts of two dimeric pairs are presumed to be originated from different crystal packing environment. It implies inherent flexibility of the hinge loop connecting the C-terminal helix. The N-terminal domain of BpHldC is attached to the main catalytic domain by forming hydrophobic core consisting of Leu15, Ile55, Val95, Leu105, and Val109. The C-terminal helix domain seems to be connected to the main catalytic domain by a hinge loop in the superfamily Burkholderia pseudomallei

Synonyms

EC Number Synonyms Comment Organism
2.7.7.70 D-glycero-beta-D-manno-heptose-1-phosphate adenylyltransferase
-
 Burkholderia pseudomallei
2.7.7.70 HldC
-
 Burkholderia pseudomallei

General Information

EC Number General Information Comment Organism
2.7.7.70 evolution BpHldC belongs to the nucleotidyltransferase alpha/beta phosphodiesterase superfamily sharing a common Rossmann-like alpha/beta fold with a conserved T/HXGH sequence motif. The invariant catalytic key residues of BpHldC indicate that the core catalytic mechanism of BpHldC may be similar to that of other closest homologues Burkholderia pseudomallei
2.7.7.70 metabolism D-glycero-beta-D-manno-heptose-1-phosphate adenylyltransferase (HldC) is the fourth enzyme of the ADP-1-glycero-beta-D-manno-heptose biosynthesis pathway, which produces an essential carbohydrate comprising the inner core of lipopolysaccharide Burkholderia pseudomallei
2.7.7.70 additional information the crystal structure of BpHldC belongs to the nucleotidyltransferase alpha/beta phosphodiesterase superfamily sharing a common Rossmann-like alpha/beta fold with a conserved T/HXGH sequence motif. The invariant catalytic key residues of BpHldC indicate that the core catalytic mechanism of BpHldC may be similar to that of other closest homologues. Intriguingly, a reorientation of the C-terminal helix seems to guide open and close states of the active site for the catalytic reaction. Active site structure analysis and structure comparisons, overview. Catalytic mechanism is inferred from the sequence and structure analysis: general, the first requirement of the nucleotidyl transfer reaction in the superfamily is to bring NTP and substrate in the proper orientation. The residues on the T/HXGH motif, flap domain and initial portion of alpha7 helix accomplish the condition by making interaction with the phosphate moieties of NTP and stabilizing the highly charged pentacovalent transition state. The catalytic activity of BpHldC may also require an adequate position of b-H1P in the correct orientation. Then, the phosphate moiety of beta-H1P undergoes nucleophilic attack on the alpha-phosphate of the ATP in an in-line displacement mechanism. The formation of the stable transition state by the key basic residues (His 40, Lys69) is presumed to be essential in the catalytic mechanism as shown in other family members Burkholderia pseudomallei