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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  18 Jul 11  (Deposition) - 10 Aug 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
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 2
    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: KDSA, KDSA2, BURPS1710B_3264
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B
    Synonym: 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHASE 2, KDO-8-PHOSPHATE SYNTHASE 2, PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE 2

 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
1ACT4Ligand/IonACETATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:13 , ARG A:183 , GLY A:230BINDING SITE FOR RESIDUE ACT A 301
2AC2SOFTWAREASN B:13 , PHE B:182 , ARG B:183 , GLY B:230BINDING SITE FOR RESIDUE ACT B 301
3AC3SOFTWAREASN C:13 , PHE C:182 , ARG C:183 , GLY C:230BINDING SITE FOR RESIDUE ACT C 301
4AC4SOFTWAREASN D:13 , PHE D:182 , ARG D:183 , GLY D:230BINDING SITE FOR RESIDUE ACT D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SZ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3SZ8)

(-) 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 Q3JP68_BURP1 | Q3JP68 from UniProtKB/TrEMBL  Length:281

    Alignment length:279
                             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         
         Q3JP68_BURP1     - -MNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSLQCRDPLGDASGGRRRQVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPAL 278
               SCOP domains d3sz8a_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeee.....---------------hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sz8 A   0 SMNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSL---------------QVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPAL 278
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  |      -       219       229       239       249       259       269         
                                                                                                                                                                                                                                    202             218                                                            


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q3JP68_BURP1 | Q3JP68 from UniProtKB/TrEMBL  Length:281

    Alignment length:280
                             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
         Q3JP68_BURP1     - -MNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSLQCRDPLGDASGGRRRQVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
               SCOP domains d3sz8b_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhh.....eeee.....--------------.hhhhhhhhhhhhh..eeeeeee......----...ee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sz8 B   0 SMNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSL--------------RQVLDLARAGIAVGIAGLFLEAHPDPDRA----PSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  |      -       219       229       239     |   -|      259       269       279
                                                                                                                                                                                                                                    202            217                         245  250                             


Chain C from PDB  Type:PROTEIN  Length:264
 aligned with Q3JP68_BURP1 | Q3JP68 from UniProtKB/TrEMBL  Length:281

    Alignment length:279
                                    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         
         Q3JP68_BURP1     1 MNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSLQCRDPLGDASGGRRRQVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
               SCOP domains d3sz8c_ C: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeee.....---------------hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sz8 C   1 MNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSL---------------QVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -       220       230       240       250       260       270         
                                                                                                                                                                                                                                   202             218                                                             


Chain D from PDB  Type:PROTEIN  Length:262
 aligned with Q3JP68_BURP1 | Q3JP68 from UniProtKB/TrEMBL  Length:281

    Alignment length:280
                             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
         Q3JP68_BURP1     - -MNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSLQCRDPLGDASGGRRRQVLDLARAGIAVGIAGLFLEAHPDPDRARCDGPSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
               SCOP domains d3sz8d_ D: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhh...eeee.........hhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhh.....eeee.....---------------hhhhhhhhhhhhh..eeeeeee.......---...ee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sz8 D   0 SMNVAISPGVTAGNSLPFVLFGGINVLESLDFTLDVCGEYVAVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLKIFAEVKARFGVPVITDVHEAEQAAPVAEIADVLQVPAFLARQTDLVVAIAKAGKPVNVKKPQFMSPTQLKHVVSKCGEVGNDRVMLCERGSSFGYDNLVVDMLGFRQMAETTGGCPVIFDVTHSL---------------QVLDLARAGIAVGIAGLFLEAHPDPDRAR---PSALPLHQLEGLLSQMKAIDDLVKRMPALE 279
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  |      -       219       229       239      |  -|      259       269       279
                                                                                                                                                                                                                                    202             218                         246 250
   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 3SZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SZ8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q3JP68_BURP1 | Q3JP68)
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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  3sz8
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 Related Entries

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

UniProtKB/TrEMBL
        Q3JP68_BURP1 | Q3JP68: 3tmq 3und

(-) Related Entries Specified in the PDB File

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