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(-) Description

Title :  CRYSTAL STRUCTURE OF R117Q MUTANT OF 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE (KDO8PS) FROM NEISSERIA MENINGITIDIS
 
Authors :  T. M. Allison, F. C. Cochrane, G. B. Jameson, E. J. Parker
Date :  23 Mar 13  (Deposition) - 26 Jun 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Manno-Octulosonate, Synthase, Lipopolysaccharide, Kdop, Kdo8 Kdops, Kdo8Ps, Tim Barrel, Transferase, Lipopolysaccharide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Allison, F. C. Cochrane, G. B. Jameson, E. J. Parker
Examining The Role Of Intersubunit Contacts In Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase.
Biochemistry V. 52 4676 2013
PubMed-ID: 23746359  |  Reference-DOI: 10.1021/BI400521F

(-) 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: 469008
    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  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:137 , GLN B:138 , ARG B:165 , HOH B:519BINDING SITE FOR RESIDUE CL B 301
2AC2SOFTWAREPRO C:137 , GLN C:138 , ARG C:165BINDING SITE FOR RESIDUE CL C 301
3AC3SOFTWAREALA C:103 , CYS C:106 , ASN C:130 , HOH C:463 , HOH C:464 , HOH C:465BINDING SITE FOR RESIDUE NA C 302
4AC4SOFTWAREALA D:113 , GLN D:138 , ARG D:165BINDING SITE FOR RESIDUE CL D 301
5AC5SOFTWAREGLN D:110 , LYS D:135 , HIS D:199BINDING SITE FOR RESIDUE CL D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JTK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JTK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JTK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JTK)

(-) Exons   (0, 0)

(no "Exon" information available for 4JTK)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains d4jtka_ A: 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....eeeehhhhh....hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jtk A   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLAQQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRGRRAQALDLALAGMATRLAGLFLELHLLEDFLIRIKALDDLIKSQPIL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  218       228       255       265       275  
                                                                                                                                                                                                                                     204|                    236|                       
                                                                                                                                                                                                                                      213                     254                       


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains d4jtkb_ B: 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...hhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtk B   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLAQQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRRRAQALDLALAGMATRLAGLFLESHLLEDFLIRIKALDDLIKSQPILTI 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  219       229       256       266       276   
                                                                                                                                                                                                                                     204|                    237|                        
                                                                                                                                                                                                                                      214                     255                        


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4jtkc_ 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.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee.hhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtk C   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLAQQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQRRAQALDLALAGMATRLAGLFLESHPALPLHLLEDFLIRIKALDDLIKSQPILT 278
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||    221       231       252       262       272      
                                                                                                                                                                                                                                   202|                      239|                           
                                                                                                                                                                                                                                    214                       251                           


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jtkd_ 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....eeeehhhhh....hhhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtk D   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLAQQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRRRAQALDLALAGMATRLAGLFLESHPALPLHLLEDFLIRIKALDDLIKSQPIL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  219       229       239|      260       270       
                                                                                                                                                                                                                                     204|                      239|                          
                                                                                                                                                                                                                                      214                       251
   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 4JTK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JTK)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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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 3stf 3stg 4jte 4jtf 4jtg 4jth 4jti 4jtj 4jtl

(-) Related Entries Specified in the PDB File

4jte 4jtf 4jtg 4jth 4jti 4jtj 4jtl