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(-) Description

Title :  SULFOLOBUS SULFATARICUS 2-KETO-3-DEOXYGLUCONATE ALDOLASE Y103F,Y130F, A198F VARIANT
 
Authors :  S. J. Crennell, S. F. Royer, M. Angelopoulou, D. W. Hough, M. J. Danson, S
Date :  18 Mar 11  (Deposition) - 28 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Tim Barrel, Biocatalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. F. Royer, S. J. Crennell, M. Angelopolou, D. W. Hough, M. J. Danson, S. D. Bull
Sulfolobus Sulfataricus 2-Keto-3-Deoxygluconate Aldolase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-KETO-3-DEOXY GLUCONATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET3A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: KDG ALDOLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2GOL5Ligand/IonGLYCEROL
3IPA2Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2GOL10Ligand/IonGLYCEROL
3IPA4Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:14 , ASP A:15 , LEU A:170 , ASN A:171 , PRO A:172 , ASN A:173 , MET A:174BINDING SITE FOR RESIDUE GOL A1294
2AC2SOFTWARELEU A:50 , PRO A:52 , GLY A:75 , LEU A:76 , ASN A:77 , ASP A:80 , TYR A:102 , HOH A:2046 , HOH A:2049 , HOH A:2061 , HOH B:2041BINDING SITE FOR RESIDUE GOL A1295
3AC3SOFTWAREARG A:32 , TYR A:63 , ASP A:64 , THR A:66 , ASN A:67 , HOH A:2057BINDING SITE FOR RESIDUE EPE A1296
4AC4SOFTWAREARG A:106 , MET A:107 , SER A:108 , HIS A:111 , GLY B:240 , SER B:241 , LEU B:242 , SER B:243BINDING SITE FOR RESIDUE GOL B1295
5AC5SOFTWAREHOH B:2181BINDING SITE FOR RESIDUE GOL B1296
6AC6SOFTWARELYS B:114 , LYS B:117 , THR B:118 , GLU B:121BINDING SITE FOR RESIDUE GOL B1297
7AC7SOFTWAREILE A:162 , SER B:180 , ASP B:181 , MET B:182 , PHE B:198 , ARG B:237BINDING SITE FOR RESIDUE IPA B1298
8AC8SOFTWAREASP B:90 , LYS B:218BINDING SITE FOR RESIDUE IPA B1299

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:120 -A:150
2B:120 -B:150

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:262 -Pro A:263
2Pro B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YDA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YDA)

(-) Exons   (0, 0)

(no "Exon" information available for 2YDA)

(-) 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:292
 aligned with KDGA_SULSF | O54288 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:292
                                    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 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILK 293
               SCOP domains d2ydaa_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh...eeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yda A   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYFYPRMSEKHLVKYFKTLCEVSPHPVYLFNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAFGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILK 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  


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 d2ydab_ B: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2yda B   2 PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYFYPRMSEKHLVKYFKTLCEVSPHPVYLFNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAFGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 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)
  - → 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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YDA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YDA)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDGA_SULSF | O54288: 1w37 1w3i 1w3n 1w3t

(-) Related Entries Specified in the PDB File

1w37 2-KETO-3-DEOXYGLUCONATE(KDG) ALDOLASE OF SULFOLOBUS SOLFATARICUS
1w3i SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE (KDG) ALDOLASE COMPLEX WITH PYRUVATE
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