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(-) Description

Title :  CRYSTAL STRUCTURE OF F114R 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 :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Manno-Octulosonate, Synthase, Lipopolysaccharide, Kdop, Kdo8 Kdops, Kdo8Ps, Tim Barrel, Biosynthesis, 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  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:177 , LEU A:179 , ASP B:172 , LEU B:174 , SER B:211 , ARG B:214 , HOH B:476BINDING SITE FOR RESIDUE GOL B 301
2AC2SOFTWAREILE B:63 , LYS B:265 , HOH B:491BINDING SITE FOR RESIDUE CL B 302
3AC3SOFTWAREALA B:113 , PRO B:137 , GLN B:138BINDING SITE FOR RESIDUE CL B 303
4AC4SOFTWAREALA C:113 , GLN C:138 , ARG C:165BINDING SITE FOR RESIDUE CL C 301
5AC5SOFTWAREGLN C:110 , LYS C:135 , HIS C:199BINDING SITE FOR RESIDUE CL C 302
6AC6SOFTWAREHOH B:495 , ALA C:103 , CYS C:106 , ASN C:130 , HOH C:426 , HOH C:434BINDING SITE FOR RESIDUE NA C 303
7AC7SOFTWAREARG C:229 , GLN C:274 , ILE C:276 , LEU C:277 , HOH C:420 , HOH C:451 , LEU D:219 , ARG D:263BINDING SITE FOR RESIDUE GOL D 301
8AC8SOFTWARELYS D:52 , GLN D:110 , LYS D:135 , HIS D:199 , PHE D:234BINDING SITE FOR RESIDUE CL D 302
9AC9SOFTWAREALA D:113 , GLN D:138 , ARG D:165BINDING SITE FOR RESIDUE CL D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JTF)

(-) 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
                                                                                                                                                                                                                                                                                          
               SCOP domains d4jtfa_ 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....eee...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtf A   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPARLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQGRRAQALDLALAGMATRLAGLFLELHLLEDFLIRIKALDDLIKSQPIL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 ||    220       230     ||257       267       277
                                                                                                                                                                                                                                   202|                    236|                       
                                                                                                                                                                                                                                    213                     254                       


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4jtfb_ B: 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.hhhhh....hhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtf B   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPARLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPALPLHLLEDFLIRIKALDDLIKSQPILTI 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       251       261       271        
                                                                                                                                                                                                                                                                        239|                            
                                                                                                                                                                                                                                                                         251                            


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4jtfc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhh....hhhhhhhhhhhhh....eeeeeee.ee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtf C   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPARLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRRRAQALDLALAGMATRLAGLFLESHALPLHLLEDFLIRIKALDDLIKSQPIL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  219       229       251       261       271      
                                                                                                                                                                                                                                     204|                     238|                          
                                                                                                                                                                                                                                      214                      251                          


Chain D from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4jtfd_ 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...hhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtf D   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPARLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRAQALDLALAGMATRLAGLFLESHPALPLHLLEDFLIRIKALDDLIKSQPIL 277
                                    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     
                                                                                                                                                                                                                                    203|                     239|                          
                                                                                                                                                                                                                                     215                      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 4JTF)

(-) Pfam Domains  (0, 0)

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

(-) 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 4jtg 4jth 4jti 4jtj 4jtk 4jtl

(-) Related Entries Specified in the PDB File

4jte 4jtg 4jth 4jti 4jtj 4jtk 4jtl