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(-) Description

Title :  CRYSTAL STRUCTURE OF KD(P)GA FROM T.TENAX
 
Authors :  A. Pauluhn, E. Pohl, E. Lorentzen, B. Siebers, H. Ahmed, S. Buchinger, D. Schomburg
Date :  12 Sep 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Aldolase, Thermophilic, X-Ray Structure, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pauluhn, H. Ahmed, E. Lorentzen, S. Buchinger, D. Schomburg, B. Siebers, E. Pohl
Crystal Structure And Stereochemical Studies Of Kd(P)G Aldolase From Thermoproteus Tenax.
Proteins V. 72 35 2008
PubMed-ID: 18186475  |  Reference-DOI: 10.1002/PROT.21890
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-KETO-3-DEOXY-(6-PHOSPHO-)GLUCONATE ALDOLASE
    Chains: A, D, B, C
    EC Number: 4.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KDGA
    Organism Scientific: THERMOPROTEUS TENAX
    Organism Taxid: 2271

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:26 , THR B:61 , THR B:62 , TYR B:148 , LYS B:173 , THR B:175BINDING SITE FOR RESIDUE SO4 B 2
2AC2SOFTWAREPRO C:26 , THR C:61 , THR C:62 , TYR C:148 , THR C:175 , HOH C:449BINDING SITE FOR RESIDUE SO4 C 3
3AC3SOFTWAREPRO A:26 , THR A:61 , THR A:62 , TYR A:148 , LYS A:173 , THR A:175BINDING SITE FOR RESIDUE SO4 A 1
4AC4SOFTWAREPRO D:26 , THR D:61 , THR D:62 , TYR D:148 , LYS D:173 , THR D:175BINDING SITE FOR RESIDUE SO4 D 4

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:138 -A:168
2B:138 -B:168
3C:138 -C:168
4D:138 -D:168

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R91)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R91)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R91)

(-) Exons   (0, 0)

(no "Exon" information available for 2R91)

(-) 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:286
 aligned with KDGA_THETE | Q704D1 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:286
                                    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       290       300      
           KDGA_THETE    21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
               SCOP domains d2r91a_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2r91A00 A:21-306 Aldolase class I                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....ee..eehhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r91 A  21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
                                    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       290       300      


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with KDGA_THETE | Q704D1 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:286
                                    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       290       300      
           KDGA_THETE    21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
               SCOP domains d2r91b_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2r91B00 B:21-306 Aldolase class I                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....ee..eehhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh...eeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r91 B  21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
                                    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       290       300      


Chain C from PDB  Type:PROTEIN  Length:286
 aligned with KDGA_THETE | Q704D1 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:286
                                    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       290       300      
           KDGA_THETE    21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
               SCOP domains d2r91c_ C: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2r91C00 C:21-306 Aldolase class I                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....ee..eehhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r91 C  21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
                                    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       290       300      


Chain D from PDB  Type:PROTEIN  Length:286
 aligned with KDGA_THETE | Q704D1 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:286
                                    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       290       300      
           KDGA_THETE    21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
               SCOP domains d2r91d_ D: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2r91D00 D:21-306 Aldolase class I                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....ee..eehhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh.eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eee.hhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r91 D  21 MEIVAPVITTFRGGRLDPELFANHVKNITSKGVDVVFVAGTTGLGPALSLQEKMELTDAATSAARRVIVQVASLNADEAIALAKYAESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKELGCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPELLAGIRDAVAAGDIERARSLQFLLDEIVESARHIGYAAAVYELVEIFQGYEAGEPRGPVYPLDPEEKAWLRAAVAKAKSQLRL 306
                                    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       290       300
   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, 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 2R91)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KDGA_THETE | Q704D1)
molecular function
    GO:0061677    2-dehydro-3-deoxy-D-gluconate aldolase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate <=> pyruvate + D-glyceraldehyde.
    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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  2r91
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  4.1.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDGA_THETE | Q704D1: 2r94

(-) Related Entries Specified in the PDB File

2r94