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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE FROM BURKHOLDERIA AMBIFARIA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  25 Jul 11  (Deposition) - 17 Aug 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1
    Chains: A, B, C, D
    EC Number: 2.5.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KDSA1, BAMMC406_2018
    Organism Scientific: BURKHOLDERIA AMBIFARIA
    Organism Taxid: 398577
    Strain: MC40-6
    Synonym: 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHASE 1, KDO-8-PHOSPHATE SYNTHASE 1, PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3T4C)

(-) Sites  (0, 0)

(no "Site" information available for 3T4C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T4C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T4C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T4C)

(-) Exons   (0, 0)

(no "Exon" information available for 3T4C)

(-) 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:264
 aligned with B1YT10_BURA4 | B1YT10 from UniProtKB/TrEMBL  Length:284

    Alignment length:284
                              1                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
         B1YT10_BURA4     - --MKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYDKANRSSGKSFRGLGMDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLPGGQGTSSGGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
               SCOP domains d3t4ca_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeee....hhhhhhhhhhhhhhhhhhh...eeee.....-------------hhhhhhhhhhhhhhhh..eeee..hhhhhhhh.....eee.hhhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh......eeeee..ee.....ee..hhhhhhhhhhh..eeee........-------....hhhhhhhhhhhhhh..eeeeeee............eee..hhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4c A  -1 GSMKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYDK-------------MDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLP-------GGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
                                     8        18        28        38        48      |  -         -|       78        88        98       108       118       128       138       148       158       168       178       188       198       | -     | 218       228       238       248       258       268       278    
                                                                                   55            69                                                                                                                                      206     214                                                                    


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with B1YT10_BURA4 | B1YT10 from UniProtKB/TrEMBL  Length:284

    Alignment length:284
                             1                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
         B1YT10_BURA4     - -MKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYDKANRSSGKSFRGLGMDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLPGGQGTSSGGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLENDF 283
               SCOP domains d3t4cb_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee......eeeeee....hhhhhhhhhhhhhhhhhhhh..eeee....--------------hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhh......eeeee..ee.....ee.hhhhhhhhhhhh..eeeehhhhh...--------...hhhhhhhhhhhhhh..eeeeeee.............ee..hhhhhhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4c B   0 SMKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYD--------------MDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLP--------GQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLENDF 283
                                     9        19        29        39        49    |    -        69        79        89        99       109       119       129       139       149       159       169       179       189       199      |  -     | 219       229       239       249       259       269       279    
                                                                                 54             69                                                                                                                                      206      215                                                                    


Chain C from PDB  Type:PROTEIN  Length:262
 aligned with B1YT10_BURA4 | B1YT10 from UniProtKB/TrEMBL  Length:284

    Alignment length:284
                              1                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
         B1YT10_BURA4     - --MKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYDKANRSSGKSFRGLGMDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLPGGQGTSSGGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
               SCOP domains d3t4cc_ C: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeee....hhhhhhhhhhhhhhhhhhhh..eeee...---------------hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhh......eeeee..ee.....ee..hhhhhhhhhhh..eeeehhhhh...-------....hhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4c C  -1 GSMKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSY---------------MDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLP-------GGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
                                     8        18        28        38        48    |    -         -|       78        88        98       108       118       128       138       148       158       168       178       188       198       | -     | 218       228       238       248       258       268       278    
                                                                                 53              69                                                                                                                                      206     214                                                                    


Chain D from PDB  Type:PROTEIN  Length:259
 aligned with B1YT10_BURA4 | B1YT10 from UniProtKB/TrEMBL  Length:284

    Alignment length:283
                             1                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
         B1YT10_BURA4     - -MKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSSYDKANRSSGKSFRGLGMDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLPGGQGTSSGGQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
               SCOP domains d3t4cd_ D: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee......eeeeee....hhhhhhhhhhhhhhhhhhh...eeee..----------------hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhh......eeeee..ee.....ee.hhhhhhhhhhhh..eeeehhhhh...--------...hhhhhhhhhhhhhh..eeeeeee.............ee..hhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4c D   0 SMKLYDFEVGLDQPFFLIAGTCVVESEQMTIDTAGRLKEICAKLNVPFIYKSS----------------MDEGLRILGEVKRQLGLPVLTDVHSIDEIEQVASVVDVLQTPAFLCRQTDFIHACARSGKPVNIKKGQFLAPHDMKNVIDKAREAAREAGLSEDRFMACERGVSFGYNNLVSDMRSLAIMRETSAPVVFDATHSVQLP--------GQREFVPVLARAAVATGVAGLFMETHPNPAEAKSDGPNAVPLNRMGALLETLVTLDQAVKRHPFLEND 282
                                     9        19        29        39        49  |      -        69        79        89        99       109       119       129       139       149       159       169       179       189       199      |  -     | 219       229       239       249       259       269       279   
                                                                               52               69                                                                                                                                      206      215
   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  (0, 0)

(no "CATH Domain" information available for 3T4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T4C)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (B1YT10_BURA4 | B1YT10)
molecular function
    GO:0008676    3-deoxy-8-phosphooctulonate synthase activity    Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + 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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019294    keto-3-deoxy-D-manno-octulosonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3t4c
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 Related Entries

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(-) Related Entries Specified in the PDB File

3sz8 STRUCTURE OF BURKHOLDERIA PSEUDOMALLEI HOMOLOG RELATED ID: BUAMA.00102.A RELATED DB: TARGETDB