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(-) Description

Title :  NEISSERIA MENINGITIDIS 3 DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE VAL223ALA VARIANT REGULATED
 
Authors :  L. C. Heyes, E. J. Parker
Date :  02 Aug 15  (Deposition) - 10 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  C,D
Keywords :  Dah7Ps, Allostery, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Heyes, E. J. Parker
Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Val223Ala Variant Regulated At 1. 70 Angstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
    Chains: C, D
    EC Number: 2.5.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21*
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Gene: AROG, NMB0307
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP B (STRAIN MC58)
    Organism Taxid: 122586
    Strain: MC58
    Synonym: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE,DAHP SYNTHASE,PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MN2Ligand/IonMANGANESE (II) ION
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PHE2Mod. Amino AcidPHENYLALANINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , HOH C:732binding site for residue MN C 401
02AC2SOFTWAREARG C:175 , ASP C:200 , HOH C:508 , THR D:102binding site for residue CL C 402
03AC3SOFTWARELYS C:188 , ARG C:236 , HIS C:270 , HOH C:704 , HOH C:725binding site for residue CL C 403
04AC4SOFTWARETYR C:96 , ALA C:163 , LYS C:188 , HOH C:574 , HOH C:733binding site for residue CL C 404
05AC5SOFTWARELYS C:216 , HOH D:573 , HOH D:580 , HOH D:836binding site for residue CL C 405
06AC6SOFTWARETYR C:26 , GLU C:27 , PHE C:123 , ARG C:126binding site for residue PEG C 406
07AC7SOFTWAREMET C:149 , GLN C:153 , ALA C:156 , GLY C:180 , LEU C:181 , SER C:182 , PHE C:211 , SER C:213 , LYS C:216 , HOH C:631 , ASP D:8 , ASP D:9binding site for residue PHE C 407
08AC8SOFTWAREARG C:55binding site for residue EDO C 408
09AC9SOFTWARETRP C:106 , GLY C:117binding site for residue EDO C 409
10AD1SOFTWARECYS D:63 , HIS D:270 , GLU D:304 , ASP D:324 , HOH D:768binding site for residue MN D 401
11AD2SOFTWARELYS D:188 , ARG D:236 , HIS D:270 , HOH D:727 , HOH D:749binding site for residue CL D 402
12AD3SOFTWARETYR D:96 , ALA D:163 , LYS D:188 , HOH D:603 , HOH D:763binding site for residue CL D 403
13AD4SOFTWARETRP D:106 , LEU D:115 , ASP D:313binding site for residue PEG D 404
14AD5SOFTWAREPHE D:123 , PEG D:406binding site for residue PEG D 405
15AD6SOFTWARETYR D:26 , GLU D:27 , PHE D:123 , ARG D:126 , PEG D:405binding site for residue PEG D 406
16AD7SOFTWAREASP C:8 , ASP C:9 , MET D:149 , GLN D:153 , ALA D:156 , GLY D:180 , LEU D:181 , SER D:182 , PHE D:211 , SER D:213 , LYS D:216 , HOH D:565 , HOH D:732binding site for residue PHE D 407
17AD8SOFTWAREARG D:101 , THR D:102 , THR D:103 , ARG D:167binding site for residue EDO D 408
18AD9SOFTWAREGLY C:330 , GLU C:333 , LEU D:307 , GLY D:328 , TRP D:329 , GLY D:330 , HOH D:626 , HOH D:672binding site for residue EDO D 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D04)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D04)

(-) Exons   (0, 0)

(no "Exon" information available for 5D04)

(-) 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 C from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d04 C   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIAHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343      


Chain D from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh....hhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d04 D   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIAHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 5D04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D04)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q9K169_NEIMB | Q9K169: 4hsn 4hso 4ixx 4uc5 4ucg 4uma 4umb 4umc 5cz0 5czs 5czt 5d02 5d03 5d05 5d09 5dcb 5dcd 5dce

(-) Related Entries Specified in the PDB File

5cz0 5czs 5czt 5d02 5d03 5d05 5d09