Structural Classification of Proteins

Fold: ATP-grasp

: Consists of two subdomains with different alpha+beta folds
shares functional and structural similarities with the PIPK and protein kinase superfamilies

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)
Fold: ATP-grasp [56058]
Consists of two subdomains with different alpha+beta folds
shares functional and structural similarities with the PIPK and protein kinase superfamilies

Superfamilies:

Glutathione synthetase ATP-binding domain-like [56059] (9)
uperfamily
1. ATP-binding domain of peptide synthetases [56060] (4)
  1. Prokaryotic glutathione synthetase, C-domain [56061]
    1. Escherichia coli [TaxId: 562] [56062] (4)
  2. D-ala-D-ala ligase, C-domain [56063]
    1. Escherichia coli, gene ddlB [TaxId: 562] [56064] (3)
  3. D-alanine:D-lactate ligase VanA, C-domain [56065]
    1. Leuconostoc mesenteroides, Ddl2 [TaxId: 1245] [56066] (1)
    2. Enterococcus faecium [TaxId: 1352] [64402] (1)
2. Lysine biosynthesis enzyme LysX ATP-binding domain [103281] (1)
  1. Lysine biosynthesis enzyme LysX ATP-binding domain [103282]
    1. Thermus thermophilus [TaxId: 274] [103283] (2)
3. BC ATP-binding domain-like [56067] (8)
  1. Biotin carboxylase (BC), domain 2 [56068]
    subunit of acetyl-CoA and pyruvate carboxylases
    1. Escherichia coli [TaxId: 562] [56069] (13)
    2. Aquifex aeolicus [TaxId: 63363] [103284] (1)
  2. Glycinamide ribonucleotide synthetase (GAR-syn), domain 2 [56070]
    1. Escherichia coli [TaxId: 562] [56071] (1)
    2. Thermotoga maritima [TaxId: 2336] [111187] (1)
      SQ Q9X0X7
  3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), domain 2 [56072]
    1. Escherichia coli [TaxId: 562] [56073] (6)
  4. Glycinamide ribonucleotide transformylase PurT, domain 2 [56074]
    1. Escherichia coli [TaxId: 562] [56075] (7)
  5. Carbamoyl phosphate synthetase (CPS), large subunit ATP-binding domains [56076]
    duplication: CPS large subunit contains two full BC-like lobes: carboxyphosphate and carbamoyl phosphate domains
    1. Escherichia coli [TaxId: 562] [56077] (10)
      SQ P00968
  6. Acetyl-CoA carboxylase, BC-M subdomain [118120]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118121] (2)
      SQ Q00955 13-566
4. Synapsin C-terminal domain [56078] (3)
  1. Synapsin [56079]
    1. Cow (Bos taurus) [TaxId: 9913] [56080] (2)
    2. Rat (Rattus norvegicus) [TaxId: 10116] [103285] (2)
  2. Synapsin II [90030]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [90031] (2)
5. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56081] (2)
  1. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56082]
    1. Escherichia coli [TaxId: 562] [56083] (18)
    2. Pig (Sus scrofa) [TaxId: 9823] [56084] (6)
      GTP-specific enzyme
6. Pyruvate phosphate dikinase, N-terminal domain [56085] (3)
  1. Pyruvate phosphate dikinase, N-terminal domain [56086]
    the common fold is interrupted by a 4-helical subdomain (residues 112-198)
    1. Clostridium symbiosum [TaxId: 1512] [56087] (7)
    2. Trypanosoma brucei [TaxId: 5691] [75557] (1)
    3. Maize (Zea mays) [TaxId: 4577] [143889] (2)
      SQ P11155 74-453
7. Eukaryotic glutathione synthetase ATP-binding domain [56088] (2)
  circularly permuted version of prokaryotic enzyme
  1. Eukaryotic glutathione synthetase ATP-binding domain [56089]
    1. Human (Homo sapiens) [TaxId: 9606] [56090] (1)
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82788] (2)
8. Glutathionylspermidine synthase ATP-binding domain-like [143890] (1)
  both terminal parts of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
  1. Glutathionylspermidine synthase, synthetase domain [143891]
    1. Escherichia coli [TaxId: 562] [143892] (10)
      SQ P0AES0 201-378,497-615
9. PurP ATP-binding domain-like [160804] (3)
  Pfam 06973; DUF1297
  1. 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP [160805]
    1. Thermococcus kodakaraensis [TaxId: 311400] [160806] (3)
      SQ Q5JD28 98-310
    2. Methanocaldococcus jannaschii [TaxId: 2190] [160807] (4)
      SQ Q57600 124-361
    3. Pyrococcus furiosus [TaxId: 2261] [160808] (12)
      SQ Q8U0R7 100-334
DNA ligase/mRNA capping enzyme, catalytic domain [56091] (4)
has a circularly permuted topology
uperfamily
1. ATP-dependent DNA ligase catalytic domain [56092] (3)
  1. ATP-dependent DNA ligase, N-terminal domain [56093]
    1. Bacteriophage T7 [TaxId: 10760] [56094] (1)
    2. Chlorella virus PBCV-1 [TaxId: 10506] [56095] (7)
  2. DNA ligase I (LIG1) [118122]
    1. Human (Homo sapiens) [TaxId: 9606] [118123] (1)
      SQ P18858 262-901
2. Adenylation domain of NAD+-dependent DNA ligase [56096] (3)
  1. Adenylation domain of NAD+-dependent DNA ligase [56097]
    contains additional, N-terminal all-alpha subdomain
    1. Bacillus stearothermophilus [TaxId: 1422] [56098] (1)
    2. Thermus filiformis [TaxId: 276] [56099] (2)
    3. Enterococcus faecalis [TaxId: 1351] [118124] (2)
      SQ Q837V6 5-317
3. mRNA capping enzyme [56100] (2)
  1. RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain [56101]
    1. Chlorella virus PBCV-1 [TaxId: 10506] [56102] (3)
  2. mRNA capping enzyme alpha subunit [90032]
    1. Yeast (Candida albicans) [TaxId: 5476] [90033] (1)
4. RNA ligase [103286] (2)
  1. RNA ligase 2, N-terminal domain [103287]
    1. Bacteriophage T4 [TaxId: 10665] [103288] (1)
  2. RNA editing ligase MP52 [118125]
    1. Trypanosoma brucei [TaxId: 5691] [118126] (1)
      SQ P82863 52-316