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(-) Description

Title :  STRUCTURE OF EPSP SYNTHASE LIGANDED WITH SHIKIMATE-3-PHOSPHATE
 
Authors :  E. Schonbrunn, S. Eschenburg, W. Shuttleworth, J. V. Schloss, N. Amrhein, J. N. S. Evans, W. Kabsch
Date :  07 Nov 00  (Deposition) - 07 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Two-Domain Structure; Inside-Out Alpha-Beta Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Schonbrunn, S. Eschenburg, W. A. Shuttleworth, J. V. Schloss, N. Amrhein, J. N. Evans, W. Kabsch
Interaction Of The Herbicide Glyphosate With Its Target Enzyme 5-Enolpyruvylshikimate 3-Phosphate Synthase In Atomic Detail.
Proc. Natl. Acad. Sci. Usa V. 98 1376 2001
PubMed-ID: 11171958  |  Reference-DOI: 10.1073/PNAS.98.4.1376
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPSP SYNTHASE
    Chains: A
    EC Number: 2.5.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AROA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1FMT13Ligand/IonFORMIC ACID
2PO41Ligand/IonPHOSPHATE ION
3S3P1Ligand/IonSHIKIMATE-3-PHOSPHATE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:22 , ASN A:94 , GLY A:96 , THR A:97 , ARG A:124 , GLN A:171 , GLU A:341 , LYS A:411 , S3P A:601 , FMT A:701 , HOH A:805 , HOH A:806BINDING SITE FOR RESIDUE PO4 A 801
02AC2SOFTWARELYS A:22 , SER A:23 , ARG A:27 , THR A:97 , SER A:169 , SER A:170 , GLN A:171 , SER A:197 , TYR A:200 , ASP A:313 , ASN A:336 , LYS A:340 , FMT A:701 , PO4 A:801 , HOH A:802 , HOH A:803 , HOH A:804BINDING SITE FOR RESIDUE S3P A 601
03AC3SOFTWARELYS A:22 , ASP A:313 , GLU A:341 , ARG A:344 , HIS A:385 , ARG A:386 , S3P A:601 , PO4 A:801BINDING SITE FOR RESIDUE FMT A 701
04AC4SOFTWAREGLU A:89 , PHE A:91 , HOH A:883 , HOH A:1154BINDING SITE FOR RESIDUE FMT A 702
05AC5SOFTWARETHR A:58 , VAL A:62 , SER A:63 , TYR A:64 , HOH A:1202 , HOH A:1295 , HOH A:1329BINDING SITE FOR RESIDUE FMT A 703
06AC6SOFTWARETYR A:382 , HOH A:919 , HOH A:988 , HOH A:1172BINDING SITE FOR RESIDUE FMT A 704
07AC7SOFTWARETHR A:65 , LEU A:66 , SER A:67 , ARG A:72 , HOH A:1176 , HOH A:1297 , HOH A:1323BINDING SITE FOR RESIDUE FMT A 705
08AC8SOFTWARELYS A:373 , LEU A:374 , SER A:397 , ASP A:398 , HOH A:1003 , HOH A:1122BINDING SITE FOR RESIDUE FMT A 706
09AC9SOFTWAREPRO A:8 , ILE A:9 , ALA A:10 , GLN A:425 , ALA A:426 , HOH A:1246BINDING SITE FOR RESIDUE FMT A 707
10BC1SOFTWAREASP A:13 , GLY A:14 , THR A:259 , HOH A:1321 , HOH A:1328BINDING SITE FOR RESIDUE FMT A 708
11BC2SOFTWARETHR A:5 , LEU A:143 , ARG A:152 , PHE A:376 , THR A:402 , HOH A:1031 , HOH A:1308BINDING SITE FOR RESIDUE FMT A 709
12BC3SOFTWAREARG A:11 , ASN A:217 , HIS A:219 , HOH A:1215BINDING SITE FOR RESIDUE FMT A 710
13BC4SOFTWARELYS A:38 , TYR A:335 , HIS A:363 , HOH A:1179 , HOH A:1335BINDING SITE FOR RESIDUE FMT A 711
14BC5SOFTWARETHR A:263 , ASP A:292 , HOH A:1230BINDING SITE FOR RESIDUE FMT A 712
15BC6SOFTWARELEU A:301 , PHE A:324 , HOH A:1160 , HOH A:1187BINDING SITE FOR RESIDUE FMT A 713

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G6T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:149 -Pro A:150
2Gly A:257 -Gly A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G6T)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPSP_SYNTHASE_1PS00104 EPSP synthase signature 1.AROA_ECOLI90-104  1A:90-104
2EPSP_SYNTHASE_2PS00885 EPSP synthase signature 2.AROA_ECOLI338-356  1A:338-356

(-) Exons   (0, 0)

(no "Exon" information available for 1G6T)

(-) 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:427
 aligned with AROA_ECOLI | P0A6D3 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:427
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
           AROA_ECOLI     1 MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTALGVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPRMKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTAPLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVEGDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGELNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVEEGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQLARISQAA 427
               SCOP domains d1g6ta_ A: 5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1g6tA01           -1g6tA02 A:20-223  [code=3.65.10.10, no name defined]                                                                                                                                                        -----------------1g6tA01 A:1-18,A:241-427  [code=3.65.10.10, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.eeee...hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeee......eeee...........eeee...hhhhhhhhhhhh......eeee.hhhhhhh.hhhhhhhhhhh...eee........eee......eeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhh....eee...eeee..........eee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhh.eeee...eeeee.......eee......hhhhhhhhhhhh...eeee.hhhhhhh..hhhhhhhhhhhhh..eeee...eeeee........ee....hhhhhhhhhhhhhh...eeee.hhhhhhh..hhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------EPSP_SYNTHASE_1-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EPSP_SYNTHASE_2    ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g6t A   1 MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTALGVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPRMKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTAPLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVEGDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGELNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVEEGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQLARISQAA 427
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G6T)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AROA_ECOLI | P0A6D3)
molecular function
    GO:0003866    3-phosphoshikimate 1-carboxyvinyltransferase activity    Catalysis of the reaction: 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate.
    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: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.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
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:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AROA_ECOLI | P0A6D3: 1eps 1g6s 1mi4 1p88 1p89 1q0i 1q0j 1q36 1x8r 1x8t 2aa9 2aay 2pq9 2qfq 2qfs 2qft 2qfu 3fjx 3fjz 3fk0 3fk1

(-) Related Entries Specified in the PDB File

1g6s EPSP SYNTHASE LIGANDED WITH SHIKIMATE-3-PHOSPHATE AND GLYPHOSATE