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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE (KDPG) ALDOLASE FROM PSEUDOMONAS PUTIDA.
 
Authors :  L. Watanabe, B. J. Bell, L. Lebioda, J. L. Rios-Steiner, A. Tulinsky, R.
Date :  03 Oct 02  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  2-Keto-3-Deoxy-6-Phosphogluconate Aldolase, Sulfate, Beta-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. J. Bell, L. Watanabe, J. L. Rios-Steiner, A. Tulinsky, L. Lebioda, R. K. Arni
Structure Of 2-Keto-3-Deoxy-6-Phosphogluconate (Kdpg) Aldolase From Pseudomonas Putida.
Acta Crystallogr. , Sect. D V. 59 1454 2003
PubMed-ID: 12876349  |  Reference-DOI: 10.1107/S0907444903013192
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KDPG ALDOLASE
    ChainsA
    EC Number4.1.2.14
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    Synonym2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:174 , GLY A:175 , THR A:195 , THR A:196 , HOH A:305BINDING SITE FOR RESIDUE SO4 A 299
2AC2SOFTWAREGLU A:57 , ARG A:61 , GLY A:84 , THR A:85 , VAL A:104 , THR A:105 , PRO A:106 , LYS A:145BINDING SITE FOR RESIDUE SO4 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MXS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:147 -Pro A:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_KDPG_KHG_1PS00159 KDPG and KHG aldolases active site.ALKD_PSEPU52-61  1A:52-61
2ALDOLASE_KDPG_KHG_2PS00160 KDPG and KHG aldolases Schiff-base forming residue.ALKD_PSEPU140-153  1A:140-153
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_KDPG_KHG_1PS00159 KDPG and KHG aldolases active site.ALKD_PSEPU52-61  3A:52-61
2ALDOLASE_KDPG_KHG_2PS00160 KDPG and KHG aldolases Schiff-base forming residue.ALKD_PSEPU140-153  3A:140-153

(-) Exons   (0, 0)

(no "Exon" information available for 1MXS)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:216
 aligned with ALKD_PSEPU | P00885 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:216
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           ALKD_PSEPU    11 LSMADKAARIDAICEKARILPVITIAREEDILPLADALAAGGIRTLEVTLRSQHGLKAIQVLREQRPELCVGAGTVLDRSMFAAVEAAGAQFVVTPGITEDILEAGVDSEIPLLPGISTPSEIMMGYALGYRRFKLFPAEISGGVAAIKAFGGPFGDIRFCPTGGVNPANVRNYMALPNVMCVGTGWMLDSSWIKNGDWARIEACSAEAIALLDAN 226
               SCOP domains d1mxsa_ A: KDPG aldolase                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxsA00 A:11-226 Aldolase class I                                                                                                                                                                                        CATH domains
               Pfam domains ---------Aldolase-1mxsA01 A:20-215                                                                                                                                                                           ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...ee....hhhhhhhhhhh...ee.ee.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.....eeee.......hhhhhhhh.....eee....hhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------ALDOLASE_K------------------------------------------------------------------------------ALDOLASE_KDPG_------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mxs A  11 LSMADKAARIDAICEKARILPVITIAREEDILPLADALAAGGIRTLEVTLRSQHGLKAIQVLREQRPELCVGAGTVLDRSMFAAVEAAGAQFVVTPGITEDILEAGVDSEIPLLPGISTPSEIMMGYALGYRRFKLFPAEISGGVAAIKAFGGPFGDIRFCPTGGVNPANVRNYMALPNVMCVGTTWMLDSSWIKNGDWARIEACSAEAIALLDAN 226
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      

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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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALKD_PSEPU | P00885)
molecular function
    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: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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