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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE FROM BRUCIELLA MELITENSIS AT 1.85A RESOLUTION
 
Authors :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  09 Jan 09  (Deposition) - 20 Jan 09  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Ssgcid, Bruciellla Melitensis, Dahp Synthetase I, 2-Dehydro- 3-Deoxyphosphooctonate Aldolase, Cytoplasm, Lipopolysaccharide Biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ssgcid
Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate Aldolase From Bruciella Melitensis At 1. 85A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    Chains: A, B
    EC Number: 2.5.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 3787797, BMEI0850, KDSA
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 29459
    Strain: BIOVAR ABORTUS 2308
    Synonym: PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3- DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO- 8-PHOSPHATE SYNTHETASE, KDO 8-P SYNTHASE, KDOPS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1PG46Ligand/IonTETRAETHYLENE GLYCOL
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:117 , ALA A:118 , LYS A:140 , ARG A:170 , HIS A:202 , HOH A:320 , HOH A:373 , HOH A:375 , HOH A:391BINDING SITE FOR RESIDUE PO4 A 278
2AC2SOFTWARELYS A:87 , LYS A:88 , GLU A:89 , TYR A:90 , GLY A:91 , HOH A:316 , HOH A:346 , PRO B:20 , ARG B:272 , HOH B:419BINDING SITE FOR RESIDUE PG4 A 279
3AC3SOFTWAREALA A:131 , ARG A:132 , GLY A:134 , GLY A:161 , ASN A:246 , ALA A:247 , PRO A:248BINDING SITE FOR RESIDUE PG4 A 280
4AC4SOFTWAREPRO B:117 , ALA B:118 , LYS B:140 , ARG B:170 , HIS B:202 , HOH B:346 , HOH B:347BINDING SITE FOR RESIDUE PO4 B 278
5AC5SOFTWAREASN A:12 , GLY A:51 , GLY A:53 , ILE A:273 , GLU B:265 , HOH B:301 , HOH B:315BINDING SITE FOR RESIDUE PG4 B 279

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FS2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:62 -Ala A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FS2)

(-) Exons   (0, 0)

(no "Exon" information available for 3FS2)

(-) 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:258
 aligned with KDSA_BRUME | Q8YHF1 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
           KDSA_BRUME     3 TANSTVKVGNVTFSNSAPLALIAGPCQMETRDHAFEMAGRLKEMTDKLGIGLVYKSSFDKANRTSLKAARGIGLEKALEVFSDLKKEYGFPVLTDIHTEEQCAAVAPVVDVLQIPAFLCRQTDLLIAAARTGRVVNVKKGQFLAPWDMKNVLAKITESGNPNVLATERGVSFGYNTLVSDMRALPIMAGLGAPVIFDATHSVQQPGGQGGSTGGQREFVETLARAAVAVGVAGLFIETHEDPDNAPSDGPNMVPIDKMPALLEKLMAFDRIAKAL 277
               SCOP domains d3fs2a_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3fs2A00 A:3-277 Aldolase class I                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee.....hhhhhhhhhhhhhhhhhhhh..eeee.......---------.hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh....eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh.....eeeee..ee.....ee...hhhhhhhh....eeeehhhhh....--------hhhhhhhhhhhhhhhh..eeeeeee.hhhhh..hhhhhee..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fs2 A   3 TANSTVKVGNVTFSNSAPLALIAGPCQMETRDHAFEMAGRLKEMTDKLGIGLVYKSSFDKAN---------IGLEKALEVFSDLKKEYGFPVLTDIHTEEQCAAVAPVVDVLQIPAFLCRQTDLLIAAARTGRVVNVKKGQFLAPWDMKNVLAKITESGNPNVLATERGVSFGYNTLVSDMRALPIMAGLGAPVIFDATHSVQQPG--------QREFVETLARAAVAVGVAGFFIETHEDPDNAPSDGPNMVPIDKMPALLEKLMAFDRIAKAL 277
                                    12        22        32        42        52        62 |       - |      82        92       102       112       122       132       142       152       162       172       182       192       202     |   -    |  222       232       242       252       262       272     
                                                                                        64        74                                                                                                                                   208      217                                                            


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with KDSA_BRUME | Q8YHF1 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:277
                                    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       
           KDSA_BRUME     1 MVTANSTVKVGNVTFSNSAPLALIAGPCQMETRDHAFEMAGRLKEMTDKLGIGLVYKSSFDKANRTSLKAARGIGLEKALEVFSDLKKEYGFPVLTDIHTEEQCAAVAPVVDVLQIPAFLCRQTDLLIAAARTGRVVNVKKGQFLAPWDMKNVLAKITESGNPNVLATERGVSFGYNTLVSDMRALPIMAGLGAPVIFDATHSVQQPGGQGGSTGGQREFVETLARAAVAVGVAGLFIETHEDPDNAPSDGPNMVPIDKMPALLEKLMAFDRIAKAL 277
               SCOP domains d3fs2b_ B: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3fs2B00 B:1-277 Aldolase class I                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eeee.....eeeee.....hhhhhhhhhhhhhhhhhhhh..eeee...---------------hhhhhhhhhhhhhhhh..eeee..hhhhhhhhh....eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh.....eeeee..ee.....ee...hhhhhhhhh...eeeehhhhh....--------hhhhhhhhhhhhhhhh..eeeeeee.hhhhh-----..ee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fs2 B   1 MVTANSTVKVGNVTFSNSAPLALIAGPCQMETRDHAFEMAGRLKEMTDKLGIGLVYKSSF---------------LEKALEVFSDLKKEYGFPVLTDIHTEEQCAAVAPVVDVLQIPAFLCRQTDLLIAAARTGRVVNVKKGQFLAPWDMKNVLAKITESGNPNVLATERGVSFGYNTLVSDMRALPIMAGLGAPVIFDATHSVQQPG--------QREFVETLARAAVAVGVAGFFIETHEDPDNA-----NMVPIDKMPALLEKLMAFDRIAKAL 277
                                    10        20        30        40        50        60         -     |  80        90       100       110       120       130       140       150       160       170       180       190       200       | -      |220       230       240      |  -  |    260       270       
                                                                                      60              76                                                                                                                                 208      217                           247   253
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FS2)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDSA_BRUME | Q8YHF1)
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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