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(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYRIBOSE PHOSPHATE ALDOLASE FROM MYCOBACTERIUM AVIUM 104 IN A SCHIFF BASE WITH AN UNKNOWN ALDEHYDE
 
Authors :  Ssgcid, Seattle Structural Genomics Center For Infectious Dis (Ssgcid)
Date :  10 Jun 10  (Deposition) - 23 Jun 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Sbri, Uw, Als Deoxyribosephosphate Aldolase, Mycobacterium Avium 104, 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, C, D
    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, GENEID 4528214 GENE LOCUS MAV_4672, MAV_4672
    Organism Scientific: MYCOBACTERIUM AVIUM
    Organism Taxid: 243243
    Strain: 104
    Synonym: PHOSPHODEOXYRIBOALDOLASE, DEOXYRIBOALDOLASE, DERA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:195 , SER D:131 , SER D:170BINDING SITE FOR RESIDUE CL A 224
2AC2SOFTWAREHIS B:71 , VAL B:72 , SER B:73 , LYS B:76 , ASP B:96 , ASP B:111 , HOH B:274BINDING SITE FOR RESIDUE EDO B 224
3AC3SOFTWAREVAL C:30 , VAL C:58 , ARG C:59BINDING SITE FOR RESIDUE EDO C 224
4AC4SOFTWAREARG B:147 , GLU B:179 , ASP C:106 , ARG C:109BINDING SITE FOR RESIDUE EDO C 225
5AC5SOFTWAREALA C:21 , THR C:22 , ALA C:23 , GLY D:98 , ALA D:99 , ALA D:102 , HOH D:286 , HOH D:478BINDING SITE FOR RESIDUE EDO D 224

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NG3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:66 -Pro A:67
2Phe B:66 -Pro B:67
3Phe C:66 -Pro C:67
4Phe D:66 -Pro D:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NG3)

(-) Exons   (0, 0)

(no "Exon" information available for 3NG3)

(-) 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:219
 aligned with DEOC_MYCA1 | A0QLL2 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
           DEOC_MYCA1     2 TPTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGAGVRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
               SCOP domains d3ng3a_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh..--.eeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ng3 A   2 TPTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGA--RVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
                                    11        21        31        41        51    |  |61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
                                                                                 56 59                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with DEOC_MYCA1 | A0QLL2 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           DEOC_MYCA1     3 PTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGAGVRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
               SCOP domains d3ng3b_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhh.----.eeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ng3 B   3 PTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQA----RVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
                                    12        22        32        42        52 |    | 62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
                                                                              54   59                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:220
 aligned with DEOC_MYCA1 | A0QLL2 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           DEOC_MYCA1     3 PTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGAGVRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
               SCOP domains d3ng3c_ C: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ng3 C   3 PTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGAGVRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDGL 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with DEOC_MYCA1 | A0QLL2 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
           DEOC_MYCA1     2 TPTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAGAGVRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDG 221
               SCOP domains d3ng3d_ D: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DeoC-3ng3D01 D:7-221                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) -----DeoC-3ng3D02 D:7-221                                                                                                                                                                                                    Pfam domains (2)
           Pfam domains (3) -----DeoC-3ng3D03 D:7-221                                                                                                                                                                                                    Pfam domains (3)
           Pfam domains (4) -----DeoC-3ng3D04 D:7-221                                                                                                                                                                                                    Pfam domains (4)
         Sec.struct. author ..hhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh.--..eeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ng3 D   2 TPTRAQLAAFVDHTLLKPEATAADVAALVTEAAELGVYAVCVSPPMVPAAVQAG--VRVASVAGFPSGKHVSAVKAHEAALAVASGAAEIDMVIDVGAALAGDLDGVRADIAAVRGAVGGAVLKVIVESSALLALADEHTLVRVCRAAEDAGADFVKTSTGFHPSGGASVRAVALMAEAVGGRLGVKASGGIRTAADALAMLDAGATRLGLSGTRAVLDG 221
                                    11        21        31        41        51   |  | 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
                                                                                55 58
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NG3)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DEOC_MYCA1 | A0QLL2)
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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  3ng3
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 Related Entries

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(-) Related Entries Specified in the PDB File

3ndo HOMOLOG FROM MYCOBACTERIUM SMEGMATIS, ALSO IN A SCHIFF BASE WITH AN UNKNOWN ALDEHYDE RELATED ID: MYAVA.00289.A RELATED DB: TARGETDB