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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE (DAHP SYNTHASE) FROM AEROPYRUM PERNIX IN COMPLEX WITH MN2+ AND PEP
 
Authors :  I. A. Shumilin, L. Zhou, J. Wu, R. W. Woodard, R. Bauerle, R. H. Kretsinger
Date :  09 Mar 06  (Deposition) - 16 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  (Beta/Alpha)8 Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Shumilin, L. Zhou, J. Wu, R. W. Woodard, R. Bauerle, R. H. Kretsinger
Crystal Structure Of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix In Complex With Mn2+ And Pep
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEOXY-7-PHOSPHOHEPTULONATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: APE0581
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: DAHP SYNTHASE, PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2PEP4Ligand/IonPHOSPHOENOLPYRUVATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:46 , HIS A:216 , GLU A:242 , ASP A:253 , PEP A:302 , HOH A:313BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWARECYS B:46 , HIS B:216 , GLU B:242 , ASP B:253 , PEP B:303 , HOH B:304BINDING SITE FOR RESIDUE MN B 301
3AC3SOFTWARECYS C:46 , HIS C:216 , GLU C:242 , ASP C:253 , PEP C:304 , HOH C:340BINDING SITE FOR RESIDUE MN C 301
4AC4SOFTWARECYS D:46 , HIS D:216 , GLU D:242 , ASP D:253 , PEP D:305 , HOH D:306BINDING SITE FOR RESIDUE MN D 301
5AC5SOFTWAREARG A:70 , LYS A:75 , GLN A:126 , GLY A:128 , ALA A:129 , ARG A:130 , LYS A:151 , ARG A:181 , HIS A:216 , GLU A:242 , MN A:301 , HOH A:313 , HOH A:318BINDING SITE FOR RESIDUE PEP A 302
6AC6SOFTWAREARG B:70 , LYS B:75 , PRO B:76 , GLU B:108 , GLN B:126 , GLY B:128 , ALA B:129 , ARG B:130 , LYS B:151 , ARG B:181 , HIS B:216 , MN B:301 , HOH B:320BINDING SITE FOR RESIDUE PEP B 303
7AC7SOFTWAREARG C:70 , LYS C:75 , PRO C:76 , GLU C:108 , GLN C:126 , GLY C:128 , ALA C:129 , ARG C:130 , LYS C:151 , ARG C:181 , HIS C:216 , MN C:301 , HOH C:340BINDING SITE FOR RESIDUE PEP C 304
8AC8SOFTWAREARG D:70 , LYS D:75 , GLN D:126 , GLY D:128 , ALA D:129 , ARG D:130 , LYS D:151 , ARG D:181 , HIS D:216 , GLU D:242 , MN D:301 , HOH D:326BINDING SITE FOR RESIDUE PEP D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VS1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VS1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VS1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VS1)

(-) Exons   (0, 0)

(no "Exon" information available for 1VS1)

(-) 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:270
 aligned with Q9YEJ7_AERPE | Q9YEJ7 from UniProtKB/TrEMBL  Length:270

    Alignment length:270
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
         Q9YEJ7_AERPE     1 MAGFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 270
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1vs1A00 A:7-276 Aldolase class I                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eee..eee.....eeeee.....hhhhhhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vs1 A   7 VAGFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 276
                                    16        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


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with Q9YEJ7_AERPE | Q9YEJ7 from UniProtKB/TrEMBL  Length:270

    Alignment length:267
                                    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       
         Q9YEJ7_AERPE     4 FKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 270
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vs1B00 B:10-276 Aldolase class I                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee..eee.....eeeee.....hhhhhhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vs1 B  10 FKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 276
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       


Chain C from PDB  Type:PROTEIN  Length:268
 aligned with Q9YEJ7_AERPE | Q9YEJ7 from UniProtKB/TrEMBL  Length:270

    Alignment length:268
                                    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        
         Q9YEJ7_AERPE     3 GFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 270
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vs1C00 C:9-276 Aldolase class I                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee..eee.....eeeee.....hhhhhhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh.eeee.hhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vs1 C   9 GFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 276
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268        


Chain D from PDB  Type:PROTEIN  Length:271
 aligned with Q9YEJ7_AERPE | Q9YEJ7 from UniProtKB/TrEMBL  Length:270

    Alignment length:271
                             1                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
         Q9YEJ7_AERPE     - -MAGFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 270
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vs1D00 D:6-276 Aldolase class I                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ----------DAHP_synth_1-1vs1D01 D:16-274                                                                                                                                                                                                                                      -- Pfam domains (1)
           Pfam domains (2) ----------DAHP_synth_1-1vs1D02 D:16-274                                                                                                                                                                                                                                      -- Pfam domains (2)
           Pfam domains (3) ----------DAHP_synth_1-1vs1D03 D:16-274                                                                                                                                                                                                                                      -- Pfam domains (3)
           Pfam domains (4) ----------DAHP_synth_1-1vs1D04 D:16-274                                                                                                                                                                                                                                      -- Pfam domains (4)
         Sec.struct. author .....................eee..eee.....eeeee.....hhhhhhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vs1 D   6 PVAGFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGEFARLMGELRWHRLL 276
                                    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
   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)

(no "SCOP Domain" information available for 1VS1)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9YEJ7_AERPE | Q9YEJ7)
molecular function
    GO:0003849    3-deoxy-7-phosphoheptulonate synthase activity    Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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