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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT (S211A) OF 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE (KDO8PS) FROM NEISSERIA MENINGITIDIS
 
Authors :  T. M. Allison, G. B. Jameson, B. J. Gloyne, E. J. Parker
Date :  09 Jul 11  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Manno-Octulosonate, Synthase, Lipopolysaccharide, Kdop, Kdo8 Kdops, Kdo8Ps, Tim Barrel, Biosynthesis, Transferase, Lyase, Lipopolysaccharide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Allison, R. D. Hutton, W. Jiao, B. J. Gloyne, E. B. Nimmo, G. B. Jameson, E. J. Parker
An Extended (Beta)7(Alpha)7 Substrate-Binding Loop Is Essential For Efficient Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase
Biochemistry V. 50 9318 2011
PubMed-ID: 21942786  |  Reference-DOI: 10.1021/BI201231E

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 2.5.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KDSA, NMB1283
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58
    Synonym: 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHASE, KDO- 8-PHOSPHATE SYNTHASE, KDO 8-P SYNTHASE, KDOPS, PHOSPHO-2-DEHYDRO-3- DEOXYOCTONATE ALDOLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:52 , GLN B:110 , LYS B:135 , PHE B:234BINDING SITE FOR RESIDUE CL B 281
2AC2SOFTWAREASN B:23 , VAL B:24 , ARG B:60 , SER B:61 , TYR B:66 , SER B:273 , HOH B:554 , HOH B:579BINDING SITE FOR RESIDUE GOL B 282
3AC3SOFTWAREHOH B:351 , ALA C:103 , CYS C:106 , ASN C:130 , HOH C:572 , HOH C:573BINDING SITE FOR RESIDUE NA C 281

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3STF)

(-) 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:250
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:276
                                    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_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPI 276
               SCOP domains d3stfa_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeee......hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee..hhhhhhhhhhh....eeeehhhhhh----------hhhhhhhhhhhhhhh....eee...----------------.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3stf A   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQ----------GRRAQALDLALAGMATRLAGLFLES----------------LHLLEDFLIRIKALDDLIKSQPI 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -  |    220       230      |  -         -   |   260       270      
                                                                                                                                                                                                                                   202        213                     237              254                      


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:278
                                    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_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILT 278
               SCOP domains d3stfb_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee..hhhhhhhhhhh....eeee......----------.hhhhhhhhhhhhhh....eee...-----------------hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stf B   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQ----------GRRAQALDLALAGMATRLAGLFLES-----------------HLLEDFLIRIKALDDLIKSQPILT 278
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -  |    220       230      |  -         -    |  260       270        
                                                                                                                                                                                                                                   202        213                     237               255                       


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    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_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPIL 277
               SCOP domains d3stfc_ C: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeee......-----------hhhhhhhhhhhhhh....eeeee..--------------...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stf C   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQ-----------RRAQALDLALAGMATRLAGLFLESH--------------PLHLLEDFLIRIKALDDLIKSQPIL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -   |   220       230       | -         -  |    260       270       
                                                                                                                                                                                                                                   202         214                     238            253                        


Chain D from PDB  Type:PROTEIN  Length:251
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:276
                                    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_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPI 276
               SCOP domains d3stfd_ D: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhhh..---------hhhhhhhhhhhhhh....eee...----------------.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3stf D   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTR---------RRAQALDLALAGMATRLAGLFLES----------------LHLLEDFLIRIKALDDLIKSQPI 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   |     -   |   220       230      |  -         -   |   260       270      
                                                                                                                                                                                                                                     204       214                    237              254
   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 3STF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KDSA_NEIMB | Q9JZ55)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSA_NEIMB | Q9JZ55: 2qkf 3fyo 3fyp 3qpy 3qpz 3qq0 3qq1 3stc 3ste 3stg 4jte 4jtf 4jtg 4jth 4jti 4jtj 4jtk 4jtl

(-) Related Entries Specified in the PDB File

3stc 3ste 3stg