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(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYRIBOSE PHOSPHATE ALDOLASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Ssgcid, Seattle Structural Genomics Center For Infectious Dis (Ssgcid)
Date :  07 Jun 10  (Deposition) - 21 Jul 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Als Collaborative Crystallography, Deoxyribosephosphate Aldolase, Mycobacterium Smegmatis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEOC, MSMEG_0922
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NH41Ligand/IonAMMONIUM ION
3UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:431BINDING SITE FOR RESIDUE NH4 A 228
2AC2SOFTWAREPRO A:142 , ASP A:146 , ARG A:149 , HOH A:462BINDING SITE FOR RESIDUE GOL A 229
3AC3SOFTWAREGLU A:137 , SER A:139 , HOH A:421BINDING SITE FOR RESIDUE GOL A 230
4AC4SOFTWAREPRO B:142 , ASP B:146 , ARG B:149 , HOH B:402 , HOH B:525BINDING SITE FOR RESIDUE GOL B 228
5AC5SOFTWAREALA B:156 , ASP B:157 , ARG B:186 , LEU B:187 , HOH B:286 , HOH B:333BINDING SITE FOR RESIDUE GOL B 229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NDO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:68 -Pro A:69
2Phe B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NDO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NDO)

(-) Exons   (0, 0)

(no "Exon" information available for 3NDO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:225
 aligned with A0QQY7_MYCS2 | A0QQY7 from UniProtKB/TrEMBL  Length:227

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
         A0QQY7_MYCS2     3 DHTRAQVAALVDHTLLKPEATPSDVTALVDEAADLGVFAVCVSPPLVSVAAGVAPSGLAIAAVAGFPSGKHVPGIKATEAELAVAAGATEIDMVIDVGAALAGDLDAVSADITAVRKAVRAATLKVIVESAALLEFSGEPLLADVCRVARDAGADFVKTSTGFHPSGGASVQAVEIMARTVGERLGVKASGGIRTAEQAAAMLDAGATRLGLSGSRAVLDGFGSA 227
               SCOP domains d3ndoa_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndo A   3 DHTRAQVAALVDHTLLKPEATPSDVTALVDEAADLGVFAVCVSPPLVSVAAGVAPSGLAIAAVAGFPSGKHVPGIKATEAELAVAAGATEIDMVIDVGAALAGDLDAVSADITAVRKAVRAATLKVIVESAALLEFSGEPLLADVCRVARDAGADFVKTSTGFHPSGGASVQAVEIMARTVGERLGVKASGGIRTAEQAAAMLDAGATRLGLSGSRAVLDGFGSA 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with A0QQY7_MYCS2 | A0QQY7 from UniProtKB/TrEMBL  Length:227

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
         A0QQY7_MYCS2     3 DHTRAQVAALVDHTLLKPEATPSDVTALVDEAADLGVFAVCVSPPLVSVAAGVAPSGLAIAAVAGFPSGKHVPGIKATEAELAVAAGATEIDMVIDVGAALAGDLDAVSADITAVRKAVRAATLKVIVESAALLEFSGEPLLADVCRVARDAGADFVKTSTGFHPSGGASVQAVEIMARTVGERLGVKASGGIRTAEQAAAMLDAGATRLGLSGSRAVLDGFGSA 227
               SCOP domains d3ndob_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DeoC-3ndoB01 B:8-223                                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -----DeoC-3ndoB02 B:8-223                                                                                                                                                                                                    ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndo B   3 DHTRAQVAALVDHTLLKPEATPSDVTALVDEAADLGVFAVCVSPPLVSVAAGVAPSGLAIAAVAGFPSGKHVPGIKATEAELAVAAGATEIDMVIDVGAALAGDLDAVSADITAVRKAVRAATLKVIVESAALLEFSGEPLLADVCRVARDAGADFVKTSTGFHPSGGASVQAVEIMARTVGERLGVKASGGIRTAEQAAAMLDAGATRLGLSGSRAVLDGFGSA 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NDO)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A0QQY7_MYCS2 | A0QQY7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004139    deoxyribose-phosphate aldolase activity    Catalysis of the reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0009264    deoxyribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0046386    deoxyribose phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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