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(-) Description

Title :  2-KETO-3-DEOXYGLUCONATE ALDOLASE FROM SULFOLOBUS ACIDOCALDARIUS IN COMPLEX WITH PYRUVATE
 
Authors :  A. Van Eerde, B. W. Dijkstra
Date :  10 Nov 06  (Deposition) - 10 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Wolterink-Van Loo, A. Van Eerde, M. A. J. Siemerink, J. Akerboom, B. W. Dijkstra, J. Van Der Oost
Biochemical And Structural Exploration Of The Catalytic Capacity Of Sulfolobus Kdg Aldolases
Biochem. J. V. 403 421 2007
PubMed-ID: 17176250  |  Reference-DOI: 10.1042/BJ20061419

(-) Compounds

Molecule 1 - 2-KETO-3-DEOXYGLUCONATE/2-KETO-3-DEOXY-6-PHOSPHO GLUCONATE ALDOLASE
    ChainsA, B
    EC Number4.1.2.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET24D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSACI_0225
    Organism ScientificSULFOLOBUS ACIDOCALDARIUS DSM 639
    Organism Taxid330779
    StrainDSM639

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:63 , HOH A:2043 , HOH A:2046 , HOH B:439 , HOH B:444 , HOH B:445BINDING SITE FOR RESIDUE MG A 2001
2AC2SOFTWAREPRO A:6 , PHE A:38 , GLY A:41 , THR A:42 , THR A:43 , TYR A:129 , LYS A:153 , GLY A:177 , VAL A:193BINDING SITE FOR RESIDUE PYR A 400
3AC3SOFTWAREPRO B:6 , PHE B:38 , GLY B:41 , THR B:42 , THR B:43 , TYR B:129 , LYS B:153 , GLY B:177 , VAL B:193 , HOH B:437BINDING SITE FOR RESIDUE PYR B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NUY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:259 -Pro A:260
2Pro B:259 -Pro B:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NUY)

(-) 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:288
 aligned with KDGA_SULAC | Q4JC35 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           KDGA_SULAC     1 MEIISPIITPFDKQGKVNVDALKTHAKNLLEKGIDAIFVNGTTGLGPALSKDEKRQNLNALYDVTHKLIFQVGSLNLNDVMELVKFSNEMDILGVSSHSPYYFPRLPEKFLAKYYEEIARISSHSLYIYNYPAATGYDIPPSILKSLPVKGIKDTNQDLAHSLEYKLNLPGVKVYNGSNTLIYYSLLSLDGVVASFTNFIPEVIVKQRDLIKQGKLDDALRLQELINRLADILRKYGSISAIYVLVNEFQGYDVGYPRPPIFPLTDEEALSLKREIEPLKRKIQELVH 288
               SCOP domains d2nuya_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nuyA00 A:1-288 Aldolase class I                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nuy A   1 MEIISPIITPFDKQGKVNVDALKTHAKNLLEKGIDAIFVNGTTGLGPALSKDEKRQNLNALYDVTHKLIFQVGSLNLNDVMELVKFSNEMDILGVSSHSPYYFPRLPEKFLAKYYEEIARISSHSLYIYNYPAATGYDIPPSILKSLPVKGIKDTNQDLAHSLEYKLNLPGVKVYNGSNTLIYYSLLSLDGVVASFTNFIPEVIVKQRDLIKQGKLDDALRLQELINRLADILRKYGSISAIYVLVNEFQGYDVGYPRPPIFPLTDEEALSLKREIEPLKRKIQELVH 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with KDGA_SULAC | Q4JC35 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           KDGA_SULAC     1 MEIISPIITPFDKQGKVNVDALKTHAKNLLEKGIDAIFVNGTTGLGPALSKDEKRQNLNALYDVTHKLIFQVGSLNLNDVMELVKFSNEMDILGVSSHSPYYFPRLPEKFLAKYYEEIARISSHSLYIYNYPAATGYDIPPSILKSLPVKGIKDTNQDLAHSLEYKLNLPGVKVYNGSNTLIYYSLLSLDGVVASFTNFIPEVIVKQRDLIKQGKLDDALRLQELINRLADILRKYGSISAIYVLVNEFQGYDVGYPRPPIFPLTDEEALSLKREIEPLKRKIQELVH 288
               SCOP domains d2nuyb_ B: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nuyB00 B:1-288 Aldolase class I                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nuy B   1 MEIISPIITPFDKQGKVNVDALKTHAKNLLEKGIDAIFVNGTTGLGPALSKDEKRQNLNALYDVTHKLIFQVGSLNLNDVMELVKFSNEMDILGVSSHSPYYFPRLPEKFLAKYYEEIARISSHSLYIYNYPAATGYDIPPSILKSLPVKGIKDTNQDLAHSLEYKLNLPGVKVYNGSNTLIYYSLLSLDGVVASFTNFIPEVIVKQRDLIKQGKLDDALRLQELINRLADILRKYGSISAIYVLVNEFQGYDVGYPRPPIFPLTDEEALSLKREIEPLKRKIQELVH 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDGA_SULAC | Q4JC35)
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_SULAC | Q4JC352nuw 2nux

(-) Related Entries Specified in the PDB File

2nuw SAME PROTEIN, NATIVE STRUCTURE
2nux