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(-) Description

Title :  CRYSTAL STRUCTURE OF S213G VARIANT DAH7PS FROM NEISSERIA MENINGITIDIS
 
Authors :  P. J. Cross, A. L. Pietersma, T. M. Allison, S. M. Wilson-Coutts, F. C. Co E. J. Parker
Date :  30 Oct 12  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dahp, Dahps, Dah7Ps, Tim Barrel, Transferase, Allosteric Regulation, Aromatic Biosynthesis, Shikimate Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Cross, A. L. Pietersma, T. M. Allison, S. M. Wilson-Coutts, F. C. Cochrane, E. J. Parker
Neisseria Meningitidis Expresses A Single 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase That I Inhibited Primarily By Phenylalanine.
Protein Sci. V. 22 1087 2013
PubMed-ID: 23754471  |  Reference-DOI: 10.1002/PRO.2293

(-) Compounds

Molecule 1 - 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.54
    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: AROG, NMB0307
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58 (SEROGROUP B)
    Synonym: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, 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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2PEP4Ligand/IonPHOSPHOENOLPYRUVATE
3TYR4Mod. Amino AcidTYROSINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:153 , LEU A:177 , GLY A:180 , LEU A:181 , SER A:182 , GLY A:213 , VAL A:214 , LYS A:216 , ASP B:8 , ASP B:9BINDING SITE FOR RESIDUE TYR 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 , GLU A:304 , MN A:403 , HOH A:501 , HOH A:564BINDING SITE FOR RESIDUE PEP A 402
03AC3SOFTWARECYS A:63 , HIS A:270 , GLU A:304 , ASP A:324 , PEP A:402BINDING SITE FOR RESIDUE MN A 403
04AC4SOFTWAREASP A:9 , GLN B:153 , GLY B:180 , LEU B:181 , SER B:182 , VAL B:214 , LYS B:216BINDING SITE FOR RESIDUE TYR B 401
05AC5SOFTWAREARG B:94 , TYR B:96 , LYS B:99 , ALA B:166 , ARG B:167 , LYS B:188 , ARG B:236 , HIS B:270 , GLU B:304 , MN B:403 , HOH B:509 , HOH B:510 , HOH B:518BINDING SITE FOR RESIDUE PEP B 402
06AC6SOFTWARECYS B:63 , HIS B:270 , GLU B:304 , ASP B:324 , PEP B:402BINDING SITE FOR RESIDUE MN B 403
07AC7SOFTWAREGLN C:153 , ALA C:156 , GLY C:180 , LEU C:181 , SER C:182 , GLY C:213 , VAL C:214 , LYS C:216 , ASP D:9 , HOH D:519BINDING SITE FOR RESIDUE TYR C 401
08AC8SOFTWAREARG C:94 , TYR C:96 , LYS C:99 , GLY C:165 , ALA C:166 , ARG C:167 , LYS C:188 , ARG C:236 , HIS C:270 , GLU C:304 , MN C:403 , HOH C:511BINDING SITE FOR RESIDUE PEP C 402
09AC9SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , PEP C:402BINDING SITE FOR RESIDUE MN C 403
10BC1SOFTWAREASP C:8 , ASP C:9 , ILE C:12 , GLN D:153 , ALA D:156 , GLY D:180 , LEU D:181 , SER D:182 , GLY D:213 , VAL D:214BINDING SITE FOR RESIDUE TYR D 401
11BC2SOFTWAREARG D:94 , TYR D:96 , LYS D:99 , GLY D:165 , ALA D:166 , ARG D:167 , LYS D:188 , ARG D:236 , HIS D:270 , GLU D:304 , MN D:403 , HOH D:512 , HOH D:515BINDING SITE FOR RESIDUE PEP D 402
12BC3SOFTWARECYS D:63 , HIS D:270 , GLU D:304 , ASP D:324 , PEP D:402BINDING SITE FOR RESIDUE MN D 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HSO)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hso A   6 PTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLGVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMARAY 401
                                    15        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    ||
                                                                                                                                                                                                                                                                                                                                                                                  350|
                                                                                                                                                                                                                                                                                                                                                                                   401


Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hso B   8 DDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLGVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMARAY 401
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  ||
                                                                                                                                                                                                                                                                                                                                                                                350|
                                                                                                                                                                                                                                                                                                                                                                                 401


Chain C from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhh..eeeeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhh....hhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hso C   5 YPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLGVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMARAY 401
                                    14        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     ||
                                                                                                                                                                                                                                                                                                                                                                                   350|
                                                                                                                                                                                                                                                                                                                                                                                    401


Chain D from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...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
                 4hso D   5 YPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLGVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMARAY 401
                                    14        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     ||
                                                                                                                                                                                                                                                                                                                                                                                   350|
                                                                                                                                                                                                                                                                                                                                                                                    401
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4HSO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HSO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q9K169_NEIMB | Q9K169: 4hsn 4ixx 4uc5 4ucg 4uma 4umb 4umc 5cz0 5czs 5czt 5d02 5d03 5d04 5d05 5d09 5dcb 5dcd 5dce

(-) Related Entries Specified in the PDB File

4hsn