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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with ?-thialysine by using a chemical mutagenesis strategy.

(2013) Chembiochem 14

PubMed: 23418011 | PubMedCentral: PMC3792637 | DOI: 10.1002/cbic.201200714

Finally, we solved the structure of the K165C variant (PDB ID: 4AHQ), and the K165-γ-thialysine enzyme with (PDB ID: 4AMA), and without (PDB ID: 4AHO) bound pyruvate.

E) The structure of the Schiff base formed between pyruvate and γ-thialysine at position 165 in the chemically modified enzyme (4AMA).

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4356361

Supplementary Material PDB reference: spermidine synthase, complex with dcAdoMet and 4MAN, 4bp3 PDB reference: complex with MTA and putrescine, 4bp1 PDB reference: complex with MTA and 4AMA, 4uoe PDB ... eference: complex with MTA and spermidine, 4cxm PDB reference: complex with BIPA, 4cwa Supporting Information.

  MTA + putrescine MTA + spermidine dcAdoMet + 4MAN MTA + 4AMA BIPA PDB code 4bp1 4cxm 4bp3 4oue 4cwa Data collection Source MAX-lab I911-2 MAX-lab I911-3 MAX-lab I911-2 MAX-lab I911-2 MAX-lab I911-2 Space group C 121 C 121 C 121 C 121 C 121 Unit-cell parameters a () 200.75 197.90 195.46 198.05 197.50 b () 34.97 134.40 132.79 135.62 134.38 c () 48.60 48.30 49.16 48.31 148.28 () 96.60 95.50 94.86 95.33 94.53 Completeness (%) 99.6 (98.7) 98.6 (98.7) 93.7 (78.5) 96.0 (94.9) 97.9 (94.2) Resolution range () 28.652.17 (2.312.17) 44.941.75 (1.861.75) 28.651.76 (1.861.76) 29.542.05 (2.102.05) 26.632.02 (2.142.02) R merge 0.12 (0.67) 0.05 (0.59) 0.05 (0.39) 0.07 (0.48) 0.09 (0.56) R meas 0.142 0.065 0.062 0.088 0.070 I /( I ) 11.0 (2.2) 15.0 (2.3) 15.4 (2.4) 14.2 (3.2) 13.2 (3.7) No.

Table 2 Ligand-validation statistics PDB code Ligand Chain R.m.s.d. † () RSCC ‡ LLDF § B iso § ( 2 ) 4bp1 MTA A AB : 0.25 0.98 0.9 23 B BC : 0.24 0.98 0.6 22 C AC : 0.24 0.98 0.2 19 Putrescine A AB : 0.48 0.91 5.0 44 B BC : 0.98 0.97 3.9 25 C AC : 1.01 0.98 3.7 23 4cxm MTA A AB : 0.20 0.99 0.9 22 B BC : 0.12 0.98 0.6 20 C AC : 0.25 0.98 1.0 17 Spermidine A AB : 0.84 0.94 1.6 34 B BC : 0.91 0.94 4.3 28 C AC : 0.25 0.96 2.6 23 4bp3 dcAdoMet A AB : 0.21 0.96 0.2 25 B BC : 0.20 0.96 0.9 22 C AC : 0.16 0.96 0.3 20 4MAN A AB : 0.10 0.96 0.5 26 B BC : 0.18 0.99 0.6 18 C AC : 0.21 0.98 0.8 15 4uoe MTA A AB : 0.24 0.97 0.3 21 B BC : 0.24 0.96 0.5 22 C AC : 0.18 0.98 0.1 23 4AMA A AB : 0.29 0.93 0.6 37 B BC : 0.32 0.96 0.9 21 C AC : 0.27 0.98 0.8 19 4cwa BIPA A AB : 0.88 2.7 41 B BC :   No ligand   C AC : 0.44 0.93 3.9 26 † R.m.s.d. calculated between corresponding ligand atoms in superimposed protein chains A , B and C .

of water molecules 410 496 391 426 352 Bound ligands 3 MTA, 3 putrescine, 1 glycerol, 1 PEG 3 MTA, 3 spermidine 3 dcAdoMet, 3 4MAN, 1 glycerol, 2 PEG 3 MTA, 3 4AMA, 2 glycerol, 1 PEG 2 BIPA, 1 PEG Average B factor ( 2 ) 28.1 25.0 23.4 28.0 27.0 Clash score 3.6 3.3 6.1 3.2 2.9 Rotamer outliers 29 [4%] 19 [2%] 20 [3%] 14 [2%] 13 [2%] Model geometry (r.m.s. deviations from ideal geometry † ) Bond lengths () 0.021 0.025 0.025 0.021 0.021 Bond angles () 2.03 2.10 2.43 1.92 1.93 Ramachandran plot Most favoured (%) 95.0 97.0 97.0 97.0 96.8 Additional allowed (%) 4.6 2.9 3.0 3.0 3.2 Disallowed (%) 0.4 [chain A , Ile235; chain B , Ser69, Glu219] 0.1 [chain A , Ile235] 0.0 0.0 0.0 † Ideal geometry for proteins (Engh Huber, 1991 ▶ ).

The four crystal structures that contain two ligands in the active site (MTA/putrescine, MTA/spermidine, MTA/4AMA and dcAdoMet/4MAN) have 100% occupancy in all three protein molecules within the asymmetric unit (Fig. 2 ▶ a ) and clear electron density for the gatekeeper loop.

X-ray crystallography was also used to study the complexes of Pf SpdS with BIPA, 4MAN and the amino derivative of 4MAN, 4-aminomethyl­aniline (4AMA).

Discussion   This work presents the structures of Pf SpdS in complex with three different ligands, 4MAN, 4AMA and BIPA, of which 4MAN has verified inhibitory activity.

Complexes of Pf SpdS with dcAdoMet/4MAN and MTA/4AMA   Crystals of Pf SpdS grown in the presence of 4MAN alone or after pre-incubation of the protein with MTA followed by incubation with 4MAN showed no electron density for the ligand in the active site.

Publication Year: 2015