SCOPe 2.05: Family c.1.11.2: D-glucarate dehydratase-like

Lineage for Family c.1.11.2: D-glucarate dehydratase-like

1. Root: SCOPe 2.05

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.1: TIM beta/alpha-barrel [51350] (33 superfamilies)
   contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
   the first seven superfamilies have similar phosphate-binding sites

4. Superfamily c.1.11: Enolase C-terminal domain-like [51604] (3 families)
   binds metal ion (magnesium or manganese) in conserved site inside barrel
   N-terminal alpha+beta domain is common to this superfamily

5. Family c.1.11.2: D-glucarate dehydratase-like [51609] (15 proteins)

Proteins:

1. beta-Methylaspartase [69400] (2 species)

   1. Species Citrobacter amalonaticus [TaxId:35703] [69402] (2 PDB entries)

   2. Species Clostridium tetanomorphum [TaxId:1553] [69401] (2 PDB entries)

2. Chlormuconate cycloisomerase [51619] (2 species)

   1. Species Alcaligenes eutrophus [TaxId:106590] [51620] (1 PDB entry)

   2. Species Pseudomonas sp. p51 [TaxId:65067] [102096] (1 PDB entry)

3. D-glucarate dehydratase [51610] (2 species)

   1. Species Escherichia coli [TaxId:562] [51612] (7 PDB entries)

   2. Species Pseudomonas putida [TaxId:303] [51611] (1 PDB entry)

4. D-mannonate dehydratase [267664] (1 species)

   • Species Escherichia coli [TaxId:199310] [267747] (1 PDB entry)

5. Hypothetical protein Atu3453 [102097] (1 species)

   • Species Agrobacterium tumefaciens [TaxId:358] [102098] (1 PDB entry)

6. Hypothetical protein Bll6730 [117384] (1 species)

   • Species Bradyrhizobium japonicum [TaxId:375] [117385] (1 PDB entry)
     Uniprot Q89FH0

7. Hypothetical protein YitF [141844] (1 species)

   • Species Bacillus subtilis [TaxId:1423] [141845] (2 PDB entries)
     Uniprot O06741 115-371

8. L-Ala-D/L-Glu epimerase [69397] (2 species)

   1. Species Bacillus subtilis [TaxId:1423] [69399] (2 PDB entries)
      Uniprot O34508

   2. Species Escherichia coli [TaxId:562] [69398] (1 PDB entry)

9. Mandelate racemase [51617] (3 species)

   1. Species Clostridium beijerinckii [TaxId:290402] [267745] (2 PDB entries)

   2. Species Dickeya dadantii [TaxId:579405] [267743] (1 PDB entry)

   3. Species Pseudomonas putida [TaxId:303] [51618] (6 PDB entries)

10. Muconate-lactonizing enzyme [51615] (1 species)

    • Species Pseudomonas putida [TaxId:303] [51616] (5 PDB entries)

11. N-acylamino acid racemase [110372] (4 species)

    1. Species Amycolatopsis sp. [TaxId:37632] [110373] (4 PDB entries)
       Uniprot Q44244 # similar activity to a remotely related O-succinylbenzoate synthase from E. coli

    2. Species Deinococcus radiodurans [TaxId:1299] [110374] (4 PDB entries)
       Uniprot Q9RYA6

    3. Species Enterococcus faecalis [TaxId:1351] [117382] (1 PDB entry)
       Uniprot Q838J7; EF0450; protein assignment by sequence similarity

    4. Species Listeria innocua [TaxId:1642] [117383] (1 PDB entry)
       Uniprot Q927X3; Lin2664; protein assignment by sequence similarity

12. O-succinylbenzoate synthase [51613] (1 species)

    • Species Escherichia coli [TaxId:562] [51614] (4 PDB entries)

13. Putative dehydratase protein STM2273 [141846] (2 species)

    1. Species Salmonella enterica [TaxId:90371] [226347] (1 PDB entry)

    2. Species Salmonella typhimurium [TaxId:90371] [141847] (1 PDB entry)
       Uniprot Q8ZNH1 123-400

14. RTS beta protein [117386] (1 species)

    • Species Xanthomonas campestris pv. campestris [TaxId:340] [117387] (1 PDB entry)
      Uniprot Q8P3K2; extended, mainly helical linker between the domains

15. automated matches [226997] (11 species)
    not a true protein

    1. Species Acidaminococcus sp. [TaxId:563191] [234735] (1 PDB entry)

    2. Species Actinobacillus succinogenes [TaxId:339671] [226437] (1 PDB entry)

    3. Species Agrobacterium tumefaciens [TaxId:176299] [226506] (4 PDB entries)

    4. Species Bradyrhizobium japonicum [TaxId:375] [255123] (2 PDB entries)

    5. Species Escherichia coli [TaxId:444449] [233282] (2 PDB entries)

    6. Species Pantoea ananatis [TaxId:706191] [267884] (1 PDB entry)

    7. Species Pectobacterium carotovorum [TaxId:561230] [267927] (1 PDB entry)

    8. Species Pseudomonas putida [TaxId:303] [228631] (6 PDB entries)

    9. Species Salmonella enterica [TaxId:550537] [267890] (3 PDB entries)

    10. Species Salmonella typhimurium [TaxId:602] [225624] (1 PDB entry)

    11. Species Vibrionales bacterium [TaxId:391574] [267878] (2 PDB entries)

More info for Family c.1.11.2: D-glucarate dehydratase-like

Timeline for Family c.1.11.2: D-glucarate dehydratase-like:

• Family c.1.11.2: D-glucarate dehydratase-like first appeared (with stable ids) in SCOP 1.55
  
• Family c.1.11.2: D-glucarate dehydratase-like appears in SCOPe 2.04
  
• Family c.1.11.2: D-glucarate dehydratase-like appears in SCOPe 2.06
  
• Family c.1.11.2: D-glucarate dehydratase-like appears in the current release, SCOPe 2.08