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(-) Description

Title :  KDPGAL COMPLEXED TO KDPGAL
 
Authors :  J. H. Naismith
Date :  02 Aug 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Lyase, Kdpgal, Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Walters, V. Srikannathasan, A. R. Mcewan, J. H. Naismith, C. A. Fierke, E. J. Toone
Characterization And Crystal Structure Of Escherichia Coli Kdpgal Aldolase.
Bioorg. Med. Chem. V. 16 710 2008
PubMed-ID: 17981470  |  Reference-DOI: 10.1016/J.BMC.2007.10.043

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
    Chains: A
    EC Number: 4.1.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 6-PHOSPHO-2-DEHYDRO-3-DEOXYGALACTONATE ALDOLASE, 2-OXO-3-DEOXYGALACTONATE 6-PHOSPHATE ALDOLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1KDP1Ligand/Ion2-KETO-DEOXY-GALACTOSE
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1KDP3Ligand/Ion2-KETO-DEOXY-GALACTOSE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:12 , ARG A:14 , THR A:66 , VAL A:85 , THR A:86 , PRO A:87 , LYS A:126 , PHE A:128 , VAL A:154 , GLY A:155 , GLY A:156 , GLY A:176 , SER A:177 , HOH A:2047 , HOH A:2061BINDING SITE FOR RESIDUE KDP A1207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V82)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:128 -Pro A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V82)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V82)

(-) Exons   (0, 0)

(no "Exon" information available for 2V82)

(-) 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:206
 aligned with DGOA_ECOLI | Q6BF16 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:206
                                                                                                                                                                                                                                     205  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   |  
           DGOA_ECOLI     2 QWQTKLPLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTVLKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKIFPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVERTAQQAAAFVKAYREAVQ--   -
               SCOP domains d2v82a_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Aldolase-2v82A01 A:2-194                                                                                                                                                                         ------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eee....hhhhhhhhhhh..eee.ee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh......eeeee......hhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v82 A   2 QWQTKLPLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTVLKPEQVDALARmGCQLIVTPNIHSEVIRRAVGYGmTVCPGCATATEAFTALEAGAQALKIFPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVERTAQQAAAFVKAYREAVQLH 207
                                    11        21        31        41        51        61        71       |81        91       101|      111       121       131       141       151       161       171       181       191       201      
                                                                                                        79-MSE                102-MSE
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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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V82)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (DGOA_ECOLI | Q6BF16)
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: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:0034194    D-galactonate catabolic process    The chemical reactions and pathways resulting in the breakdown of D-galactonate, the anion of D-galactonic acid.
    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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  4.1.2.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        DGOA_ECOLI | Q6BF16: 2v81 4qcc

(-) Related Entries Specified in the PDB File

2j6n THE NATIVE STRUCTURE OF KDPGAL ALDOLASE
2j6q THE NATIVE STRUCTURE OF KDPGAL ALDOLASE
2v81 NATIVE KDPGAL STRUCTURE