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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXOGLUTARATE ALDOLASE (TM0066) FROM THERMOTOGA MARITIMA AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Aug 04  (Deposition) - 24 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x)
Keywords :  Tm0066, 2-Dehydro-3-Deoxyphosphogluconate Aldolase/4-Hydroxy-2- Oxoglutarate Aldolase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of 2-Dehydro-3-Deoxyphosphogluconate Aldolase/4-Hydroxy-2-Oxoglutarate Aldolase (Tm0066) From Thermotoga Maritima At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2- OXOGLUTARATE ALDOLASE
    Chains: A, B, C
    EC Number: 4.1.2.14, 4.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0066
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1VLW)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:165 -A:203
2B:165 -B:203
3C:165 -C:203

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:131 -Pro A:132
2Phe B:131 -Pro B:132
3Phe C:131 -Pro C:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VLW)

(-) 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:205
 aligned with Q9WXS1_THEMA | Q9WXS1 from UniProtKB/TrEMBL  Length:205

    Alignment length:205
                              1                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     
         Q9WXS1_THEMA     - --MKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGC 203
               SCOP domains d1vlwa_ A: KDPG aldolase                                                                                                                                                                                      SCOP domains
               CATH domains 1vlwA00 A:-1-203 Aldolase class I                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...ee....hhhhhhhhhhh...ee.ee.hhhhhhhhhhh...eeee......hhhhhhhhhh.....eeee.......hhhhhhhh....eeehhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlw A  -1 HHMKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGC 203
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q9WXS1_THEMA | Q9WXS1 from UniProtKB/TrEMBL  Length:205

    Alignment length:207
                               1                                                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       
         Q9WXS1_THEMA     - ---MKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCT 204
               SCOP domains d1vlwb_ B: KDPG aldolase                                                                                                                                                                                        SCOP domains
               CATH domains 1vlwB00 B:-2-204 Aldolase class I                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eee....hhhhhhhhhhhh.eee.ee.hhhhhhhhhhh...eeee......hhhhhhhhhh.....eeee.......hhhhhhhhh...eeehhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlw B  -2 HHHMKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCT 204
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       


Chain C from PDB  Type:PROTEIN  Length:204
 aligned with Q9WXS1_THEMA | Q9WXS1 from UniProtKB/TrEMBL  Length:205

    Alignment length:204
                             1                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199    
         Q9WXS1_THEMA     - -MKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGC 203
               SCOP domains d1vlwc_ C: KDPG aldolase                                                                                                                                                                                     SCOP domains
               CATH domains 1vlwC00 C:0-203 Aldolase class I                                                                                                                                                                             CATH domains
           Pfam domains (1) ---Aldolase-1vlwC01 C:3-197                                                                                                                                                                           ------ Pfam domains (1)
           Pfam domains (2) ---Aldolase-1vlwC02 C:3-197                                                                                                                                                                           ------ Pfam domains (2)
           Pfam domains (3) ---Aldolase-1vlwC03 C:3-197                                                                                                                                                                           ------ Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eee....hhhhhhhhhhhh.eee.ee.hhhhhhhhhhh...eeee......hhhhhhhhhh.....eeee.......hhhhhhhh....eeehhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vlw C   0 HMKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGC 203
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9WXS1_THEMA | Q9WXS1)
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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  Cis Peptide Bonds
    Phe A:131 - Pro A:132   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q9WXS1_THEMA | Q9WXS1: 1wa3 5kp9

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