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(-) Description

Title :  STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITORS IN COMPLEX WITH NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE - THE IMPORTANCE OF ACCOMMODATING THE ACTIVE SITE WATER
 
Authors :  L. C. Heyes, S. Reichau, P. J. Cross, E. J. Parker
Date :  16 May 14  (Deposition) - 08 Oct 14  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Dah7Ps, Dahps, Aromatic Amino Acids, Shikimate Pathway, Oxocarbenium Ion, Meningitis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Heyes, S. Reichau, P. J. Cross, G. B. Jameson, E. J. Parker
Structural Analysis Of Substrate-Mimicking Inhibitors In Complex With Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - The Importance Of Accommodating The Active Site Water.
Bioorg. Chem. V. 57 242 2014
PubMed-ID: 25245459  |  Reference-DOI: 10.1016/J.BIOORG.2014.08.003

(-) 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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: NEISSERIA MENINGITIDIS
    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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
10V54Ligand/Ion(2R)-2-(PHOSPHONOOXY)PROPANOIC ACID
2MN4Ligand/IonMANGANESE (II) ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS C:63 , HIS C:270 , GLU C:304 , ASP C:324 , 0V5 C:1351BINDING SITE FOR RESIDUE MN C1350
02AC2SOFTWARECYS B:63 , HIS B:270 , GLU B:304 , ASP B:324 , 0V5 B:1351 , HOH B:2012BINDING SITE FOR RESIDUE MN B1350
03AC3SOFTWARECYS A:63 , HIS A:270 , GLU A:304 , ASP A:324 , 0V5 A:1353BINDING SITE FOR RESIDUE MN A1351
04AC4SOFTWARECYS D:63 , HIS D:270 , GLU D:304 , ASP D:324 , 0V5 D:1351BINDING SITE FOR RESIDUE MN D1350
05AC5SOFTWAREARG A:101 , THR A:102 , HOH A:2186BINDING SITE FOR RESIDUE PO4 A1352
06AC6SOFTWARECYS C:63 , ARG C:94 , TYR C:96 , LYS C:99 , GLU C:145 , GLY C:165 , ALA C:166 , ARG C:167 , LYS C:188 , ARG C:236 , HIS C:270 , GLU C:304 , ASP C:324 , MN C:1350 , HOH C:2051 , HOH C:2077 , HOH C:2093 , HOH C:2098BINDING SITE FOR RESIDUE 0V5 C1351
07AC7SOFTWARECYS D:63 , ARG 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:1350 , HOH D:2049 , HOH D:2073 , HOH D:2085 , HOH D:2087BINDING SITE FOR RESIDUE 0V5 D1351
08AC8SOFTWARECYS A:63 , ARG 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 , ASP A:324 , MN A:1351 , HOH A:2057 , HOH A:2092 , HOH A:2109 , HOH A:2114BINDING SITE FOR RESIDUE 0V5 A1353
09AC9SOFTWARECYS B:63 , ARG B:94 , 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 , ASP B:324 , MN B:1350 , HOH B:2012 , HOH B:2034 , HOH B:2067 , HOH B:2078 , HOH B:2080BINDING SITE FOR RESIDUE 0V5 B1351
10BC1SOFTWAREARG B:101 , THR B:102 , HOH B:2041 , HOH B:2043BINDING SITE FOR RESIDUE PO4 B1352
11BC2SOFTWAREARG C:101 , THR C:102BINDING SITE FOR RESIDUE PO4 C1352
12BC3SOFTWAREARG D:101 , THR D:102BINDING SITE FOR RESIDUE PO4 D1352

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UMB)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhh..eeeeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh.eeeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4umb A  16 KELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMARA 350
                                    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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh..eeeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4umb B  17 ELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    26        36        46        56        66        76        86        96       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   


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.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhhh.eeeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4umb C  17 ELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    26        36        46        56        66        76        86        96       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   


Chain D 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.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee........ee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4umb D  17 ELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKEPNYDAEHVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELLALLAGANKKRMAR 349
                                    26        36        46        56        66        76        86        96       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
   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)

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(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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

(-) Related Entries Specified in the PDB File

4uma STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITORS IN COMPLEX WITH NEISSERIA MENINGITIDIS 3 DEOXY D ARABINO HEPTULOSONATE 7 PHOSPHATE SYNTHASE THE IMPORTANCE OF ACCOMMODATING THE ACTIVE SITE WATER
4umc STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITORS IN COMPLEX WITH NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABINO- HEPTULOSONATE 7-PHOSPHATE SYNTHASE - THE IMPORTANCE OF ACCOMMODATING THE ACTIVE SITE WATER