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(-) Description

Title :  UNIQUE TETRAMERIC STRUCTURE OF DEOXYRIBOSE PHOSPHATE ALDOLASE FROM AEROPYRUM PERNIX
 
Authors :  H. Tsuge, H. Sakuraba, I. Shimoya, N. Katunuma, H. Ago, M. Miyano, T. Ohs Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Nov 02  (Deposition) - 25 Mar 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Aldolase, A. Pernix, Tetramer, Alpha-Beta Tim Barrel, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakuraba, H. Tsuge, I. Shimoya, R. Kawakami, S. Goda, Y. Kawarabayasi, N. Katunuma, H. Ago, M. Miyano, T. Ohshima
The First Crystal Structure Of Archaeal Aldolase. Unique Tetrameric Structure Of 2-Deoxy-D-Ribose-5-Phosphate Aldolase From The Hyperthermophilic Archaea Aeropyrum Pernix.
J. Biol. Chem. V. 278 10799 2003
PubMed-ID: 12529358  |  Reference-DOI: 10.1074/JBC.M212449200

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N7K)

(-) Sites  (0, 0)

(no "Site" information available for 1N7K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N7K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:81 -Pro A:82
2Phe B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N7K)

(-) Exons   (0, 0)

(no "Exon" information available for 1N7K)

(-) Sequences/Alignments

Asymmetric 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:234
 aligned with DEOC_AERPE | Q9Y948 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           DEOC_AERPE     2 PSARDILQQGLDRLGSPEDLASRIDSTLLSPRATEEDVRNLVREASDYGFRCAVLTPVYTVKISGLAEKLGVKLCSVIGFPLGQAPLEVKLVEAQTVLEAGATELDVVPHLSLGPEAVYREVSGIVKLAKSYGAVVKVILEAPLWDDKTLSLLVDSSRRAGADIVKTSTGVYTKGGDPVTVFRLASLAKPLGMGVKASGGIRSGIDAVLAVGAGADIIGTSSAVKVLESFKSLV 235
               SCOP domains d1n7ka_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                             SCOP domains
               CATH domains 1n7kA00 A:2-235 Aldolase class I                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh.eeee......hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n7k A   2 PSARDILQQGLDRLGSPEDLASRIDSTLLSPRATEEDVRNLVREASDYGFRCAVLTPVYTVKISGLAEKLGVKLCSVIGFPLGQAPLEVKLVEAQTVLEAGATELDVVPHLSLGPEAVYREVSGIVKLAKSYGAVVKVILEAPLWDDKTLSLLVDSSRRAGADIVKTSTGVYTKGGDPVTVFRLASLAKPLGMGVKASGGIRSGIDAVLAVGAGADIIGTSSAVKVLESFKSLV 235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with DEOC_AERPE | Q9Y948 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           DEOC_AERPE     2 PSARDILQQGLDRLGSPEDLASRIDSTLLSPRATEEDVRNLVREASDYGFRCAVLTPVYTVKISGLAEKLGVKLCSVIGFPLGQAPLEVKLVEAQTVLEAGATELDVVPHLSLGPEAVYREVSGIVKLAKSYGAVVKVILEAPLWDDKTLSLLVDSSRRAGADIVKTSTGVYTKGGDPVTVFRLASLAKPLGMGVKASGGIRSGIDAVLAVGAGADIIGTSSAVKVLESFKSLV 235
               SCOP domains d1n7kb_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                             SCOP domains
               CATH domains 1n7kB00 B:2-235 Aldolase class I                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ------------------DeoC-1n7kB01 B:20-230                                                                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) ------------------DeoC-1n7kB02 B:20-230                                                                                                                                                                                              ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhheeee......hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n7k B   2 PSARDILQQGLDRLGSPEDLASRIDSTLLSPRATEEDVRNLVREASDYGFRCAVLTPVYTVKISGLAEKLGVKLCSVIGFPLGQAPLEVKLVEAQTVLEAGATELDVVPHLSLGPEAVYREVSGIVKLAKSYGAVVKVILEAPLWDDKTLSLLVDSSRRAGADIVKTSTGVYTKGGDPVTVFRLASLAKPLGMGVKASGGIRSGIDAVLAVGAGADIIGTSSAVKVLESFKSLV 235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEOC_AERPE | Q9Y948)
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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
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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