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(-) Description

Title :  NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE REGULATED (TYROSINE)
 
Authors :  L. C. Heyes, E. Parker
Date :  24 Aug 15  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Allostery, Aromatic Amino Acid, Regulated, Ligand, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Heyes, E. J. Parker
Structure Of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated And Complexed With Pep At 2. 05 Angstroms
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 Taxid: 562
    Gene: AROG, NMB0307
    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, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3TMO4Ligand/IonTRIMETHYLAMINE OXIDE
4TYR4Mod. Amino AcidTYROSINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , HIS A:270 , GLU A:304 , ASP A:324 , HOH A:580binding site for residue MN A 401
02AC2SOFTWAREGLU A:240 , PRO A:241 , HIS A:247binding site for residue SO4 A 402
03AC3SOFTWAREALA A:166 , ARG A:167 , LYS A:188 , ARG A:236 , HIS A:270 , HOH A:587 , HOH A:589binding site for residue TMO A 403
04AC4SOFTWAREGLN A:153 , ALA A:156 , GLY A:180 , LEU A:181 , SER A:182 , SER A:213 , VAL A:214 , LYS A:216 , VAL A:223 , ASP B:8 , ASP B:9binding site for residue TYR A 404
05AC5SOFTWARECYS B:63 , HIS B:270 , GLU B:304 , ASP B:324binding site for residue MN B 401
06AC6SOFTWAREGLY B:165 , ALA B:166 , ARG B:167 , LYS B:188 , ARG B:236 , HIS B:270binding site for residue TMO B 402
07AC7SOFTWAREASP A:8 , ASP A:9 , GLN B:153 , GLY B:180 , LEU B:181 , SER B:182 , SER B:213 , VAL B:214 , VAL B:223binding site for residue TYR B 403
08AC8SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , HOH C:573binding site for residue MN C 401
09AC9SOFTWAREALA C:166 , ARG C:167 , LYS C:188 , ARG C:236 , HIS C:270binding site for residue TMO C 402
10AD1SOFTWAREGLN C:153 , ALA C:156 , GLY C:180 , LEU C:181 , SER C:182 , SER C:213 , VAL C:214 , HOH C:531 , ASP D:8 , ASP D:9binding site for residue TYR C 403
11AD2SOFTWARECYS D:63 , ARG D:94 , HIS D:270 , GLU D:304 , ASP D:324binding site for residue MN D 401
12AD3SOFTWAREGLY D:165 , ALA D:166 , LYS D:188 , ARG D:236 , HOH D:572binding site for residue TMO D 402
13AD4SOFTWAREASP 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:214 , VAL D:223 , HOH D:531binding site for residue TYR D 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCD)

(-) 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.......hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcd A   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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.......hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhh..eeeeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcd B   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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.........................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcd C   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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.........................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeee......hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcd D   4 HYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 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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  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 5DCD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

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

(-) Related Entries Specified in the PDB File

5dcb 5dce