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(-) Description

Title :  SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE (KDG) ALDOLASE COMPLEX WITH PYRUVATE
 
Authors :  A. Theodossis, H. Walden, E. J. Westwick, H. Connaris, H. J. Lamble, D. W. Hough, M. J. Danson, G. L. Taylor
Date :  15 Jul 04  (Deposition) - 02 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldolase, Archaeal Metabolism, Pyruvate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Theodossis, H. Walden, E. J. Westwick, H. Connaris, H. J. Lamble, D. W. Hough, M. J. Danson, G. L. Taylor
The Structural Basis For Substrate Promiscuity In 2-Keto-3-Deoxygluconate Aldolase From The Entner-Doudoroff Pathway In Sulfolobus Solfataricus
J. Biol. Chem. V. 279 43886 2004
PubMed-ID: 15265860  |  Reference-DOI: 10.1074/JBC.M407702200

(-) Compounds

Molecule 1 - 2-KETO-3-DEOXY GLUCONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3-A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: EDA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:7 , PHE A:39 , GLY A:42 , THR A:43 , THR A:44 , TYR A:130 , LYS A:155 , VAL A:196BINDING SITE FOR RESIDUE PYR A1295
02AC2SOFTWAREPRO B:7 , PHE B:39 , GLY B:42 , THR B:43 , THR B:44 , TYR B:130 , LYS B:155 , VAL B:196BINDING SITE FOR RESIDUE PYR B1295
03AC3SOFTWAREPRO C:7 , PHE C:39 , GLY C:42 , THR C:43 , THR C:44 , TYR C:130 , LYS C:155 , VAL C:196BINDING SITE FOR RESIDUE PYR C1295
04AC4SOFTWAREPRO D:7 , PHE D:39 , GLY D:42 , THR D:43 , THR D:44 , TYR D:130 , LYS D:155 , VAL D:196 , GOL D:1296BINDING SITE FOR RESIDUE PYR D1295
05AC5SOFTWAREGLY A:240 , SER A:241 , LEU A:242 , SER A:243 , ARG D:106 , MET D:107 , SER D:108 , HIS D:111BINDING SITE FOR RESIDUE GOL A1296
06AC6SOFTWARECYS A:120 , HIS A:125 , PRO A:126 , CYS A:150 , HOH A:2207BINDING SITE FOR RESIDUE GOL A1297
07AC7SOFTWAREGLY B:240 , SER B:241 , LEU B:242 , SER B:243 , ARG C:106 , MET C:107 , SER C:108 , HIS C:111 , HOH C:2081BINDING SITE FOR RESIDUE GOL B1296
08AC8SOFTWAREHIS B:125 , PRO B:126 , HOH B:2124 , HOH B:2224BINDING SITE FOR RESIDUE GOL B1297
09AC9SOFTWARETHR C:43 , THR C:44 , TYR C:132 , HOH C:2099 , HOH C:2208 , HOH C:2209BINDING SITE FOR RESIDUE GOL C1296
10BC1SOFTWAREARG B:106 , MET B:107 , SER B:108 , HIS B:111 , GLY C:240 , SER C:241 , LEU C:242 , SER C:243 , ILE C:264BINDING SITE FOR RESIDUE GOL C1297
11BC2SOFTWARELYS A:110 , HIS C:125 , PRO C:126 , HOH C:2210 , HOH C:2211 , ASP D:268BINDING SITE FOR RESIDUE GOL C1298
12BC3SOFTWARECYS C:120 , HIS C:125 , PRO C:126 , VAL C:127 , HOH C:2117BINDING SITE FOR RESIDUE GOL C1299
13BC4SOFTWARETHR D:43 , THR D:44 , TYR D:132 , THR D:157 , LEU D:242 , PYR D:1295 , HOH D:2111 , HOH D:2233 , HOH D:2234BINDING SITE FOR RESIDUE GOL D1296
14BC5SOFTWAREMET A:107 , SER A:108 , HIS A:111 , GLY D:240 , SER D:241 , LEU D:242 , SER D:243BINDING SITE FOR RESIDUE GOL D1297

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:120 -A:150
2B:120 -B:150
3C:120 -C:150
4D:120 -D:150

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:262 -Pro A:263
2Pro B:262 -Pro B:263
3Pro C:262 -Pro C:263
4Pro D:262 -Pro D:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W3I)

(-) Exons   (0, 0)

(no "Exon" information available for 1W3I)

(-) Sequences/Alignments

Asymmetric/Biological 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:293
 aligned with KDGA_SULSF | O54288 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           KDGA_SULSF     2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
               SCOP domains d1w3ia_ A: 2-keto-3-deoxy gluconate aldolase Eda                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w3iA00 A:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee....hhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w3i A   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with KDGA_SULSF | O54288 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           KDGA_SULSF     2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
               SCOP domains d1w3ib_ B: 2-keto-3-deoxy gluconate aldolase Eda                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w3iB00 B:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee....hhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w3i B   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain C from PDB  Type:PROTEIN  Length:293
 aligned with KDGA_SULSF | O54288 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           KDGA_SULSF     2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
               SCOP domains d1w3ic_ C: 2-keto-3-deoxy gluconate aldolase Eda                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w3iC00 C:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w3i C   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain D from PDB  Type:PROTEIN  Length:293
 aligned with KDGA_SULSF | O54288 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           KDGA_SULSF     2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
               SCOP domains d1w3id_ D: 2-keto-3-deoxy gluconate aldolase Eda                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w3iD00 D:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w3i D   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W3I)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KDGA_SULSF | O54288)
molecular function
    GO:0008674    2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity    Catalysis of the reaction: 6-phospho-2-dehydro-3-deoxy-D-galactonate = D-glyceraldehyde 3-phosphate + pyruvate.
    GO:0008675    2-dehydro-3-deoxy-phosphogluconate aldolase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.
    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: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: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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  KDGA_SULSF | O54288
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDGA_SULSF | O54288: 1w37 1w3n 1w3t 2yda

(-) Related Entries Specified in the PDB File

1w37 2-KETO-3-DEOXYGLUCONATE(KDG) ALDOLASE OF SULFOLOBUS SOLFATARICUS
1w3n SULFOLOBUS SOLFATARICUS 2-KETO-3- DEOXYGLUCONATE (KDG) ALDOLASE COMPLEX WITH D- KDG
1w3t SULFOLOBUS SOLFATARICUS 2-KETO-3- DEOXYGLUCONATE (KDG) ALDOLASE COMPLEX WITH D- KDGAL, D-GLYCERALDEHYDE AND PYRUVATE