Primary Citation PubMed: 11062559
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Divergence and convergence in enzyme evolution.
(2012) J Biol Chem 287
PubMed: 22069324 | PubMedCentral: PMC3249071 | DOI: 10.1074/jbc.R111.241976
ATP-grasp superfamily Glutathione synthetase ( 1gsh , 2hgs ), d -ala- d -Ala ligase ( 1iov ), d -Ala- d -lactate ligase ( 1e4e ), biotin carboxylase ( 1dv1 ), carba... oyl-phosphate synthase ( 1jdb ), pyruvate-phosphate dikinase ( 1dik ), phosphoribosylamine-glycine ligase PurD ( 1gso ), phosphoribosylglycinamide formyltransferase PurT ( 1eyz ), N 5 -carboxyaminoimidazole ribonucleotide synthase PurK ( 1b6s ), 5-formaminoimidazole-4-carboxamide ribonucleotide synthase PurP ( 2r7k ), tubulin-tyrosine ligase, tubulin glycylase, tubulin polyglutamylase, ribosomal protein S6-glutamate ligase RimK, succinate-CoA ligase ( 1jkj ), ATP-citrate synthase ( 3mwd ), malate-CoA ligase, synapsin ( 1aux ), α-aminoadipate-LysW ligase LysX ( 1uc9 ), glutathionylspermidine synthetase GspS ( 2io9 ), d -aspartate ligase Asl fm , carnosine synthase, γ-F420–2:α- l -glutamate ligase CofF, tetrahydromethanopterin:α- l -glutamate ligase MptN, alanine-anticapsin ligase BacD/YwfE, l -amino acid ligase, N -acetylaspartylglutamate synthase, β-citrylglutamate synthase, nikkomycin biosynthesis carboxylase SanS, inositol-1,3,4-trisphosphate 5/6-kinase ( 1z2n ), mycosporine glycine synthetase Ava_3856 Conserved structural core (≤4.3 Å Cα r.m.s.d. on ≥230 aa); common ATP-binding residues, which include two conserved Lys/Arg residues that bind α- and β-phosphates of ATP, Glx/Asp residue that interacts with adenine amino group and N6 atom, hydrophobic residues that bind adenine ring, and three Glx/Asx residues that coordinate Mg 2+ ions; common catalytic mechanism that includes formation of phosphoacyl intermediate 27 , 29 , 63 – 65 AlkP superfamily Alkaline phosphatase ( 1alk ), phosphoglycerate mutase ( 1o98 , 2zkt ), phosphopentomutase ( 3ot9 ), acid phosphatase ( 2d1g ), nucleotide pyrophosphatase/phosphodiesterase ( 2gso ), arylsulfatase ( 1auk ), N -acetylgalactosamine 4-sulfatase ( 1fsu ), steryl-sulfatase ( 1p49 ), phosphonoacetate hydrolase ( 1ei6 ), phosphoglycerol transferase MdoB, phosphonate monoester hydrolase/phosphodiesterase ( 2vqr ), GPI phosphoethanolamine transferase PIG-N/Mcd4, LPS:phosphoethanolamine transferase EptB, polyglycerol-phosphate lipoteichoic acid synthase LtaS ( 2w8d ), pilin phospho-form transferase PptA, inorganic pyrophosphatase Conserved structural core (≤3.6 Å Cα r.m.s.d. on ≥220 aa); conserved metal (Zn 2+ , Mn 2+ , or Mg 2+ )-binding His and Asp residues; common catalytic mechanism that includes phosphorylation (sulfatation) of active site Ser/Thr/fGly residue 31 – 35 , 38 – 40 Cupin superfamily Oxalate oxidase ( 1fi2 ), oxalate decarboxylase ( 1uw8 ), gentisate 1,2-dioxygenase ( 2d40 ), homogentisate 1,2-dioxygenase ( 1ey2 ), 3-hydroxyanthranilate 3,4-dioxygenase ( 1yfu ), cysteine dioxygenase ( 3eln ), quercetin 2,3-dioxygenase ( 1juh ), acetylacetone dioxygenase Dke1 ( 3bal ), 1,2-dihydroxy-3-keto-5-methylthiopentene (acireductone) dioxygenase ( 1vr3 ), 1-hydroxy-2-naphthoate dioxygenase, phosphomannose isomerase ( 1pmi ), glucose-6-phosphate isomerase ( 1qy4 ), d -lyxose isomerase, 5-keto-4-deoxyuronate isomerase KduI ( 1xru ), dTDP-4-dehydrorhamnose 3,5-epimerase RmlC ( 1dzr ), dTDP-4-keto-6-deoxyglucose 5-epimerase EvaD ( 1oi6 ), dTDP-6-deoxy-3,4-ketohexulose isomerase FdtA (2pa7 ), ectoine synthase, ureidoglycolate hydrolase ( 1yqc ), hydroxypropylphosphonic acid epoxidase ( 2bnm ), dimethylsulfoniopropionate lyase DddL, phaseolin ( 2phl ), canavalin ( 2cau ), pirin ( 1j1l ), auxin-binding protein ( 1lrh ), ethanolamine utilization protein EutQ ( 2pyt ), polyketide cyclase RemF ( 3ht1 ), bacilysin biosynthesis protein BacB ( 3h7j ), cuproprotein CucA ( 2xla ), vitamin K-dependent γ-carboxylase Conserved structural core (<4.6 Å Cα r.m.s.d. on >99 aa); partly conserved metal (Mn 2+ , Fe 2+ , Cu 2+ , Ni 2+ , or Zn 2+ )-binding His residues that often form G X 5 H XH X 3,4 E X 6 G and GD X 4 P X G X 2 H X 3 N motifs; common catalytic mechanism that includes binding of dioxygen to metal atom and substrate with formation of peroxidic intermediate 41 – 44 HD domain phosphohydrolase superfamily 3′,5′-cAMP/cGMP phosphodiesterase ( 2hd1 ), (p)ppGpp hydrolase ( 1vj7 ), cyclic di-GMP phosphodiesterase ( 3tm8 ), exopolyphosphatase ( 1u6z ), dNMP 5′-nucleotidase YfbR ( 2par ), dNTP triphosphohydrolase ( 2dqb ), dGTPase ( 3bg2 ), cyanamide hydratase, 7,8-dihydro- d -neopterin 2′,3′-cyclic phosphate phosphodiesterase MJ0837, 2′,3′-cAMP/cGMP hydrolase, 3′-5′ exoribonuclease YhaM, uridylyl-removing enzyme GlnD, myo -inositol oxygenase MioX ( 2huo ) Conserved structural core (<3.6 Å Cα r.m.s.d. on >105 aa); conserved metal (Mn 2+ , Mg 2+, Co 2+ , or Fe 2+ )-binding His and Asp residues organized into H X 20–50 HD X 60–140 D motif 45 – 50 Ntn hydrolase superfamily Penicillin acylase ( 1pnl ), glutamine 5-phosphoribosyl-1-pyrophosphate amidotransferase ( 1ecc ), proteasome subunit ( 1pma ), glucosamine-6-phosphate synthase ( 1xff ), protease Hs1V ( 1m4y ), aspartylglucosaminidase ( 1apy ), γ-glutamyltranspeptidase ( 2dg5 ), asparagine synthetase B ( 1ct9 ), β-lactam synthetase ( 1jgt ), glutamate synthase ( 1ea0 ), l -asparaginase ( 2gez ), threonine aspartase ( 2a8i ), acyl-CoA:isopenicillin N -acyltransferase ( 2x1c ), bile salt hydrolase ( 2hez ), N -acylhomoserine lactone acylase PvdQ ( 2wyb ), acid ceramidase, IMP cyclohydrolase PurO ( 2ntk ) Common structural core (<4.1 Å Cα r.m.s.d. on >96 aa) decorated with variety of structural elements; sequence conservation limited to N-terminal β-hairpin that contains catalytic Ser, Cys, or Thr residue 51 – 55 ATP-grasp The original description of the ATP-grasp superfamily featured five enzymes with very similar three-domain structures (each featuring an α+β-sandwich) and several other enzymes assigned to that superfamily based solely on conserved sequence motifs ( 26 , 27 ).
Publication Year: 2012
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.
(2012) BMC Bioinformatics 13
PubMed: 22783946 | PubMedCentral: PMC3458898 | DOI: 10.1186/1471-2105-13-162
Table 3 Non-binding sites negative dataset, composed of random surface pockets that do not bind any ligand PDB ID Cavity center PDB ID Cavity center PDB ID Cavity center 1A04 1424, 2671 1A0I 1689, 799... 1A22 2927 1AA7 579 1AF7 631, 1492 1AM2 1277 1ARO 154, 1663 1ATG 1751 1C3G 630, 888 1C3P 1089, 1576 1DXJ 867, 1498 1EVT 2149, 2229 1FI2 1493 1KLM 4373, 4113 1KWP 1212 1QZ7 3592, 2509 1YQZ 4458, 4269 1YVB 1546, 1814 1ZT9 1056, 1188 2A1K 2758, 3345 2AUP 2246 2BG9 14076, 8076 2C9Q 777 2CL3 123, 948 2DN2 749, 1006 2F1K 316, 642 2G50 26265, 31672 2G69 248, 378 2GRK 369, 380 2GSE 337, 10618 2GSH 6260 The table lists the protein’s PDB ID and the specified cavity center, computed as the centroid of the reported PDB atom numbers.
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