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(-) Description

Title :  COMPARISON OF CLASS I ALDOLASE BINDING SITE ARCHITECTURE BASED ON THE CRYSTAL STRUCTURE OF 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE DETERMINED AT 0.99 ANGSTROM RESOLUTION
 
Authors :  A. Heine, J. G. Luz, C. H. Wong, I. A. Wilson
Date :  14 Apr 03  (Deposition) - 01 Jun 04  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta Barrel, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Heine, J. G. Luz, C. H. Wong, I. A. Wilson
Analysis Of The Class I Aldolase Binding Site Architecture Based On The Crystal Structure Of 2-Deoxyribose-5-Phosphate Aldolase At 0. 99A Resolution.
J. Mol. Biol. V. 343 1019 2004
PubMed-ID: 15476818  |  Reference-DOI: 10.1016/J.JMB.2004.08.066

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    ChainsA, B
    EC Number4.1.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneB4381, DEOC, DEOC OR DRA OR THYR OR B4381 OR C5465, DRA, JW4344, THYR
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
    StrainK12
    SynonymDERA, 2-DEOXY-D-RIBOSE 5-PHOSPHATE ALDOLASE, PHOSPHODEOXYRIBOALDOLASE, DEOXYRIBOALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1P1X)

(-) Sites  (0, 0)

(no "Site" information available for 1P1X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P1X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:76 -Pro A:77
2Phe B:1076 -Pro B:1077

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P1X)

(-) Exons   (0, 0)

(no "Exon" information available for 1P1X)

(-) 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:250
 aligned with DEOC_ECOLI | P0A6L0 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
          DEOC_ECOLI      1 MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH  250
               SCOP domains d1p1xa_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                             SCOP domains
               CATH domains 1p1xA00 A:1-250 Aldolase class I                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p1x A    1 MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH  250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with DEOC_ECOLI | P0A6L0 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:251
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
          DEOC_ECOLI      - -MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH  250
               SCOP domains d1p1xb_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                              SCOP domains
               CATH domains 1p1xB00 B:1000-1250 Aldolase class I                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) ----------DeoC-1p1xB01 B:1010-1246                                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) ----------DeoC-1p1xB02 B:1010-1246                                                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh.eeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1p1x B 1000 HMTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH 1250
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249 

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: DeoC (21)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEOC_ECOLI | P0A6L0)
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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEOC_ECOLI | P0A6L01jcj 1jcl 1ktn 5eky 5el1 5emu

(-) Related Entries Specified in the PDB File

1jcj 1jcl