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(-) Description

Title :  OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION
 
Authors :  A. Heine, G. Desantis, J. G. Luz, M. Mitchell, C. -H. Wong, I. A. Wilson
Date :  09 Jun 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Heine, G. Desantis, J. G. Luz, M. Mitchell, C. H. Wong, I. A. Wilson
Observation Of Covalent Intermediates In An Enzyme Mechanism At Atomic Resolution.
Science V. 294 369 2001
PubMed-ID: 11598300  |  Reference-DOI: 10.1126/SCIENCE.1063601
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HPD2Ligand/Ion1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HPD1Ligand/Ion1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HPD1Ligand/Ion1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:102 , LYS A:167 , THR A:170 , ALA A:203 , GLY A:204 , GLY A:205 , GLY A:236 , ALA A:237 , SER A:238 , HOH A:604 , HOH A:611 , HOH A:614 , HOH A:645 , HOH A:677 , HOH A:852 , HOH A:868BINDING SITE FOR RESIDUE HPD A 601
2AC2SOFTWAREASP B:102 , LYS B:167 , THR B:170 , ALA B:203 , GLY B:204 , GLY B:205 , GLY B:236 , ALA B:237 , SER B:238 , HOH B:609 , HOH B:610 , HOH B:617 , HOH B:674 , HOH B:682 , HOH B:689BINDING SITE FOR RESIDUE HPD B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JCJ)

(-) 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:252
 aligned with DEOC_ECOLI | P0A6L0 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:252
                             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     - -MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGHG 251
               SCOP domains d1jcja_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                               SCOP domains
               CATH domains 1jcjA00 A:0-251 Aldolase class I                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhheeee......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
                 1jcj A   0 HMTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFLPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGHG 251
                                     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  


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 d1jcjb_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                              SCOP domains
               CATH domains 1jcjB00 B:0-250 Aldolase class I                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ----------DeoC-1jcjB01 B:10-246                                                                                                                                                                                                                        ---- Pfam domains (1)
           Pfam domains (2) ----------DeoC-1jcjB02 B:10-246                                                                                                                                                                                                                        ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhheeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh..........eee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jcj B   0 HMTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMMEVIRDMGVEKTVGFLPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLLKALGH 250
                                     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
   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  (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

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        DEOC_ECOLI | P0A6L0: 1jcl 1ktn 1p1x 5eky 5el1 5emu

(-) Related Entries Specified in the PDB File

1jcl OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION