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(-) Description

Title :  NEISSERIA MENINGITIDIS 3 DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE GLU176GLN VARIANT
 
Authors :  L. C. Heyes
Date :  02 Aug 15  (Deposition) - 10 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Allostery, Dah7Ps, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Heyes
Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Glu176Gln Variant At 1. 87 Angstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 2.5.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    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

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MN4Ligand/IonMANGANESE (II) ION
3PEP4Ligand/IonPHOSPHOENOLPYRUVATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , HIS A:270 , GLU A:304 , ASP A:324 , PEP A:402 , HOH A:532binding site for residue MN A 401
02AC2SOFTWAREARG A:94 , TYR A:96 , LYS A:99 , GLU A:145 , GLY A:165 , ALA A:166 , ARG A:167 , LYS A:188 , ARG A:236 , HIS A:270 , MN A:401 , HOH A:532 , HOH A:536 , HOH A:605 , HOH A:624binding site for residue PEP A 402
03AC3SOFTWAREARG A:101 , THR A:102 , HOH A:519 , HOH A:606binding site for residue SO4 A 403
04AC4SOFTWARECYS B:63 , HIS B:270 , GLU B:304 , ASP B:324 , PEP B:402 , HOH B:614binding site for residue MN B 401
05AC5SOFTWAREARG B:94 , TYR B:96 , LYS B:99 , GLU B:145 , GLY B:165 , ALA B:166 , ARG B:167 , LYS B:188 , ARG B:236 , HIS B:270 , GLU B:304 , MN B:401 , HOH B:508 , HOH B:521 , HOH B:614 , HOH B:616binding site for residue PEP B 402
06AC6SOFTWAREILE A:222 , ASP B:120 , ILE B:121 , ASN B:122binding site for residue EDO B 403
07AC7SOFTWARELEU B:115binding site for residue EDO B 404
08AC8SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , HOH C:502binding site for residue MN C 401
09AC9SOFTWAREARG C:94 , GLU C:145 , GLY C:165 , ALA C:166 , ARG C:167 , LYS C:188 , ARG C:236 , HIS C:270 , HOH C:501 , HOH C:502 , HOH C:513 , HOH C:547 , HOH C:616binding site for residue PEP C 402
10AD1SOFTWAREHIS C:224binding site for residue EDO C 403
11AD2SOFTWARESER C:31 , LEU C:133 , ASN C:137 , HOH C:512binding site for residue EDO C 404
12AD3SOFTWARECYS D:63 , HIS D:270 , GLU D:304 , ASP D:324 , PEP D:402 , HOH D:522binding site for residue MN D 401
13AD4SOFTWAREARG D:94 , TYR D:96 , LYS D:99 , GLU D:145 , GLY D:165 , ALA D:166 , ARG D:167 , LYS D:188 , ARG D:236 , HIS D:270 , GLU D:304 , MN D:401 , HOH D:503 , HOH D:522 , HOH D:535 , HOH D:556 , HOH D:558binding site for residue PEP D 402
14AD5SOFTWAREARG D:101 , ARG D:311 , THR D:323 , ASP D:324 , SO4 D:404 , HOH D:502binding site for residue EDO D 403
15AD6SOFTWAREARG D:101 , THR D:102 , EDO D:403 , HOH D:571binding site for residue SO4 D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D02)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D02)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D02)

(-) Exons   (0, 0)

(no "Exon" information available for 5D02)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh.eeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeee.....eeeee......eeeee........hhhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d02 A  16 KELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRQLASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeee......eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d02 B  15 VKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRQLASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344     


Chain C from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeee......eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh....hhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d02 C  16 KELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRQLASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    25        35        45        55        65        75        85        95       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346   
                                                                                                                  104|                                                                                                                                                                                                                                                   
                                                                                                                   106                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh.eeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh.eeeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d02 D  16 KELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRQLASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
   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 5D02)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D02)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D02)

(-) 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 5d03 5d04 5d05 5d09 5dcb 5dcd 5dce

(-) Related Entries Specified in the PDB File

5cz0 5czs 5czt 5d03 5d04 5d05 5d09