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(-) Description

Title :  NEISSERIA MENINGITIDIS 3 DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE LYS107ALA 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 :  1.75
Chains :  Asym./Biol. Unit :  A,B,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 Lys107Ala Variant Regulated At 1. 75 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 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

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 23)

Asymmetric/Biological Unit (7, 23)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MN4Ligand/IonMANGANESE (II) ION
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PEP4Ligand/IonPHOSPHOENOLPYRUVATE
5PGE1Ligand/IonTRIETHYLENE GLYCOL
6PHE4Mod. Amino AcidPHENYLALANINE
7SO44Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , HIS A:270 , GLU A:304 , ASP A:324 , HOH A:521binding site for residue MN A 401
02AC2SOFTWARELYS A:216binding site for residue CL A 402
03AC3SOFTWAREARG A:94 , GLU A:145 , LYS A:188 , ARG A:236 , HIS A:270 , HOH A:512 , HOH A:521 , HOH A:546 , HOH A:652 , HOH A:653 , HOH A:694binding site for residue PEP A 403
04AC4SOFTWARETYR A:26binding site for residue SO4 A 404
05AC5SOFTWARELEU A:115 , ASP A:116 , GLY A:117 , ASP A:313 , HOH A:764binding site for residue PGE A 405
06AC6SOFTWAREMET A:149 , GLN A:153 , ALA A:156 , GLY A:180 , LEU A:181 , SER A:182 , PHE A:211 , SER A:213 , LYS A:216 , HOH A:577 , ASP B:8 , ASP B:9binding site for residue PHE A 406
07AC7SOFTWARECYS B:63 , HIS B:270 , GLU B:304 , ASP B:324 , HOH B:519binding site for residue MN B 401
08AC8SOFTWARETRP B:106 , LEU B:115 , ASP B:116 , GLY B:117binding site for residue PEG B 402
09AC9SOFTWARESER A:208 , HIS A:209 , HOH A:536 , HOH A:555 , GLY B:105 , PHE B:119 , HOH B:526 , HOH B:648binding site for residue PEG B 403
10AD1SOFTWAREARG B:94 , TYR B:96 , LYS B:99 , GLU B:145 , LYS B:188 , ARG B:236 , HIS B:270 , HOH B:519 , HOH B:543 , HOH B:589 , HOH B:593 , HOH B:596 , HOH B:632 , HOH B:638binding site for residue PEP B 404
11AD2SOFTWAREARG B:256 , ALA B:257 , GLY B:259binding site for residue SO4 B 405
12AD3SOFTWARETYR B:26 , HOH B:682binding site for residue SO4 B 406
13AD4SOFTWAREASP A:8 , ASP A:9 , MET B:149 , GLN B:153 , ALA B:156 , GLY B:180 , LEU B:181 , SER B:182 , SER B:213 , HOH B:620 , HOH B:732binding site for residue PHE B 407
14AD5SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , HOH C:516binding site for residue MN C 401
15AD6SOFTWARETRP C:106 , LEU C:115binding site for residue PEG C 402
16AD7SOFTWAREARG C:94 , TYR C:96 , LYS C:99 , GLU C:145 , LYS C:188 , ARG C:236 , HIS C:270 , HOH C:516 , HOH C:550 , HOH C:555 , HOH C:566 , HOH C:588 , HOH C:607 , HOH C:680binding site for residue PEP C 403
17AD8SOFTWAREMET C:149 , GLN C:153 , ALA C:156 , GLY C:180 , LEU C:181 , SER C:182 , PHE C:211 , SER C:213 , HOH C:562 , HOH C:751 , ASP D:8 , ASP D:9binding site for residue PHE C 404
18AD9SOFTWARECYS D:63 , HIS D:270 , GLU D:304 , ASP D:324 , HOH D:506binding site for residue MN D 401
19AE1SOFTWAREHOH C:737 , HOH C:826 , LYS D:216binding site for residue CL D 402
20AE2SOFTWAREARG C:167 , HOH C:546 , GLU D:170 , GLN D:172 , ARG D:175binding site for residue CL D 403
21AE3SOFTWAREARG D:94 , TYR D:96 , LYS D:99 , GLU D:145 , LYS D:188 , ARG D:236 , HIS D:270 , HOH D:506 , HOH D:507 , HOH D:512 , HOH D:587 , HOH D:616 , HOH D:625binding site for residue PEP D 404
22AE4SOFTWARETYR D:26 , GLU D:27binding site for residue SO4 D 405
23AE5SOFTWAREASP C:8 , ASP C:9 , MET D:149 , GLN D:153 , ALA D:156 , GLY D:180 , LEU D:181 , SER D:182 , SER D:213 , VAL D:223 , HOH D:545 , HOH D:652binding site for residue PHE D 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D05)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D05)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D05)

(-) Exons   (0, 0)

(no "Exon" information available for 5D05)

(-) 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 ........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d05 A   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWAGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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 B 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.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d05 B   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWAGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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 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.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d05 C   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWAGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhh..eeeeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d05 D   3 HHYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWAGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5D05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D05)

(-) Gene Ontology  (8, 8)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

5czs 5czt 5d02 5d03 5d04 5d09