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(-) Description

Title :  DAHP (3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE) SYNTHASE IN COMPLEX WITH DAHP OXIME.
 
Authors :  P. Berti, M. Junop, N. Balachandran
Date :  15 Jul 15  (Deposition) - 10 Aug 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dahp Synthase, Inhibitor, Complex, Transition State Mimic, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Balachandran, M. Heimhalt, P. Liuni, F. To, D. J. Wilson, M. S. Junop P. J. Berti
Potent Inhibition Of 3-Deoxy-D-Arabinoheptulosonate-7-Phosphate (Dahp) Synthase By Dahp Oxime, A Phosphate Group Mimic.
Biochemistry V. 55 6617 2016
PubMed-ID: 27933795  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00930

(-) Compounds

Molecule 1 - PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, PHE-SENSITIVE
    Chains: A, B, C, D
    EC Number: 2.5.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell: BL21(DE3)
    Expression System Plasmid: PET300
    Expression System Taxid: 562
    Gene: AROG, B0754, JW0737
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Other Details: FIRST 5 RESIDUES ARE UNSTRUCTURED IN THE CRYSTAL STRUCTURE. ALSO LOOPS 101-102 AND 313-317.
    Strain: K12
    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  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
152L2Ligand/IonDAHP OXIME
2GAL3Ligand/IonBETA-D-GALACTOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:96 , LYS A:105 , ILE A:108 , ASN A:109 , ASP A:146 , THR A:149 , HOH A:531 , HOH A:552 , GLN B:170 , VAL B:171 , GLU B:174 , PHE B:209 , LEU B:210 , HOH B:556binding site for residue GAL A 401
2AC2SOFTWARELYS B:70 , ASP B:132 , HOH B:568 , HOH B:697 , ARG D:75 , LEU D:305 , TYR D:320 , TRP D:331binding site for residue GAL B 401
3AC3SOFTWARECYS B:61 , ARG B:92 , TYR B:94 , LYS B:97 , PRO B:98 , ARG B:99 , THR B:100 , LYS B:186 , HIS B:268 , ASP B:326 , HOH B:501 , HOH B:502 , HOH B:539 , HOH B:591 , HOH B:672 , HOH B:705binding site for residue 52L B 402
4AC4SOFTWAREGLN C:170 , GLU C:174 , PHE C:209 , LEU C:210 , HOH C:505 , HOH C:551 , GLU D:96 , ILE D:108 , ASN D:109 , ASP D:146 , THR D:149 , HOH D:463binding site for residue GAL C 401
5AC5SOFTWARECYS C:61 , ARG C:92 , TYR C:94 , LYS C:97 , PRO C:98 , ARG C:99 , THR C:100 , LYS C:186 , HIS C:268 , ASP C:326 , HOH C:502 , HOH C:524 , HOH C:534 , HOH C:556 , HOH C:561 , HOH C:611binding site for residue 52L C 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CKS)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.......................hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh.eeee.hhhh.hhhhhhhhhh....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee.......ee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cks A   5 NDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    14        24        34        44        54        64        74        84        94     ||106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     ||321       331       341         
                                                                                                                         100|                                                                                                                                                                                                              312|                                
                                                                                                                          103                                                                                                                                                                                                               318                                


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee...........................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cks B   6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    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     


Chain C from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhhhh...eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee........................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cks C   5 NDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    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       317       327       337       347   
                                                                                                                                                                                                                                                                                                                                             312|                                  
                                                                                                                                                                                                                                                                                                                                              316                                  


Chain D from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh.eeee.hhhh.hhhhhhhhhhh...eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee...eeee............ee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cks D   6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5CKS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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        AROG_ECOLI | P0AB91: 1gg1 1kfl 1n8f 1qr7

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