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(-) Description

Title :  TETRAMERIC STRUCTURE OF ALDOLASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. K. Lokanath, I. Shiromizu, M. Miyano, S. Yokoyama, S. Kuramitsu, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Jan 03  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Schiff Base, Deoxyribose Phospahte, Carbinolamine, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, I. Shiromizu, N. Ohshima, Y. Nodake, M. Sugahara, S. Yokoyama, S. Kuramitsu, M. Miyano, N. Kunishima
Structure Of Aldolase From Thermus Thermophilus Hb8 Showing The Contribution Of Oligomeric State To Thermostability.
Acta Crystallogr. , Sect. D V. 60 1816 2004
PubMed-ID: 15388928  |  Reference-DOI: 10.1107/S0907444904020190
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALDOLASE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J2W)

(-) Sites  (0, 0)

(no "Site" information available for 1J2W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J2W)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:63 -Pro A:64
2Phe B:63 -Pro B:64
3Phe C:63 -Pro C:64
4Phe D:63 -Pro D:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J2W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J2W)

(-) Exons   (0, 0)

(no "Exon" information available for 1J2W)

(-) 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:212
 aligned with DEOC_THET8 | Q5SJ28 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           DEOC_THET8     1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALVA 212
               SCOP domains d1j2wa_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                       SCOP domains
               CATH domains 1j2wA00 A:1-212 Aldolase class I                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2w A   1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALVA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with DEOC_THET8 | Q5SJ28 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           DEOC_THET8     1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALV 211
               SCOP domains d1j2wb_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                      SCOP domains
               CATH domains 1j2wB00 B:1-211 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2w B   1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALV 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with DEOC_THET8 | Q5SJ28 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           DEOC_THET8     1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALVA 212
               SCOP domains d1j2wc_ C: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                       SCOP domains
               CATH domains 1j2wC00 C:1-212 Aldolase class I                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2w C   1 MDLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALVA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain D from PDB  Type:PROTEIN  Length:210
 aligned with DEOC_THET8 | Q5SJ28 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           DEOC_THET8     2 DLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALV 211
               SCOP domains d1j2wd_ D: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                     SCOP domains
               CATH domains 1j2wD00 D:2-211 Aldolase class I                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhh.eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2w D   2 DLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVRVAQGRAQVKAAGGIRDRETALRMLKAGASRLGTSSGVALV 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J2W)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DEOC_THET8 | Q5SJ28)
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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  Cis Peptide Bonds
    Phe A:63 - Pro A:64   [ RasMol ]  
    Phe B:63 - Pro B:64   [ RasMol ]  
    Phe C:63 - Pro C:64   [ RasMol ]  
    Phe D:63 - Pro D:64   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DEOC_THET8 | Q5SJ28: 1ub3

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