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(-) Description

Title :  STRUCTURE OF 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE FROM PYROBACULUM AEROPHILUM
 
Authors :  H. Sakuraba, T. Ohshima, H. Tsuge
Date :  15 Mar 04  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Dera, Aldolase, Deoxyribose, Hyperthermophile, Archaea, 2- Deoxyribose-5-Phosphate Aldolase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakuraba, K. Yoneda, K. Yoshihara, K. Satoh, R. Kawakami, Y. Uto, H. Tsuge, K. Takahashi, H. Hori, T. Ohshima
Sequential Aldol Condensation Catalyzed By Hyperthermophili 2-Deoxy-D-Ribose-5-Phosphate Aldolase
Appl. Environ. Microbiol. V. 73 7427 2007
PubMed-ID: 17905878  |  Reference-DOI: 10.1128/AEM.01101-07

(-) Compounds

Molecule 1 - PROBABLE DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773
    Synonym: 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE, PHOSPHODEOXYRIBOALDOLASE, DEOXYRIBOALDOLASE, DERA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:3 , ASP B:211BINDING SITE FOR RESIDUE ZN B 1001
2AC2SOFTWAREASP A:211 , HIS B:3BINDING SITE FOR RESIDUE ZN A 1002

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:35 -A:54
2B:35 -B:54

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:59 -Pro A:60
2Phe B:59 -Pro B:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCV)

(-) 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:226
 aligned with DEOC_PYRAE | Q8ZXK7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           DEOC_PYRAE     1 MIHLVDYALLKPYLTVDEAVAGARKAEELGVAAYCVNPIYAPVVRPLLRKVKLCVVADFPFGALPTASRIALVSRLAEVADEIDVVAPIGLVKSRRWAEVRRDLISVVGAAGGRVVKVITEEPYLRDEERYTLYDIIAEAGAHFIKSSTGFAEEAYAARQGNPVHSTPERAAAIARYIKEKGYRLGVKMAGGIRTREQAKAIVDAIGWGEDPARVRLGTSTPEALL 226
               SCOP domains d1vcva1 A:1-226 Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                SCOP domains
               CATH domains 1vcvA00 A:1-226 Aldolase class I                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhh......hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcv A   1 MIHLVDYALLKPYLTVDEAVAGARKAEELGVAAYCVNPIYAPVVRPLLRKVKLCVVADFPFGALPTASRIALVSRLAEVADEIDVVAPIGLVKSRRWAEVRRDLISVVGAAGGRVVKVITEEPYLRDEERYTLYDIIAEAGAHFIKSSTGFAEEAYAARQGNPVHSTPERAAAIARYIKEKGYRLGVKMAGGIRTREQAKAIVDAIGWGEDPARVRLGTSTPEALL 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with DEOC_PYRAE | Q8ZXK7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           DEOC_PYRAE     1 MIHLVDYALLKPYLTVDEAVAGARKAEELGVAAYCVNPIYAPVVRPLLRKVKLCVVADFPFGALPTASRIALVSRLAEVADEIDVVAPIGLVKSRRWAEVRRDLISVVGAAGGRVVKVITEEPYLRDEERYTLYDIIAEAGAHFIKSSTGFAEEAYAARQGNPVHSTPERAAAIARYIKEKGYRLGVKMAGGIRTREQAKAIVDAIGWGEDPARVRLGTSTPEALL 226
               SCOP domains d1vcvb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 1vcvB00 B:1-226 Aldolase class I                                                                                                                                                                                                   CATH domains
           Pfam domains (1) DeoC-1vcvB01 B:1-213                                                                                                                                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) DeoC-1vcvB02 B:1-213                                                                                                                                                                                                 ------------- Pfam domains (2)
         Sec.struct. author hhh.eeee......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhh......hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcv B   1 MIHLVDYALLKPYLTVDEAVAGARKAEELGVAAYCVNPIYAPVVRPLLRKVKLCVVADFPFGALPTASRIALVSRLAEVADEIDVVAPIGLVKSRRWAEVRRDLISVVGAAGGRVVKVITEEPYLRDEERYTLYDIIAEAGAHFIKSSTGFAEEAYAARQGNPVHSTPERAAAIARYIKEKGYRLGVKMAGGIRTREQAKAIVDAIGWGEDPARVRLGTSTPEALL 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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  (2, 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  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEOC_PYRAE | Q8ZXK7)
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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