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(-) Description

Title :  CRYSTAL STRUCTURE OF CHORISMATE SYNTHASE COMPLEXED WITH FMN
 
Authors :  H. J. Ahn, H. J. Yoon, B. Lee, S. W. Suh
Date :  18 Sep 03  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Alpha-Beta Sandwich Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Ahn, H. J. Yoon, B. Lee, S. W. Suh
Crystal Structure Of Chorismate Synthase: A Novel Fmn-Binding Protein Fold And Functional Insights
J. Mol. Biol. V. 336 903 2004
PubMed-ID: 15095868  |  Reference-DOI: 10.1016/J.JMB.2003.12.072
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHORISMATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROC
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE PHOSPHOLYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:103 , HIS A:104 , ARG A:123 , SER A:125 , LEU A:240 , ASN A:241 , GLY A:242 , LYS A:296 , THR A:298 , PRO A:299 , SER A:300 , ILE A:327 , ARG A:330 , HOH A:1420 , HOH A:1432 , HOH A:1436 , HOH A:1529 , LEU D:280 , GLY D:281BINDING SITE FOR RESIDUE FMN A 1400
2AC2SOFTWARESER B:103 , HIS B:104 , ARG B:123 , SER B:125 , LEU B:240 , ASN B:241 , LYS B:296 , THR B:298 , PRO B:299 , SER B:300 , ILE B:327 , ARG B:330 , HOH B:2411 , HOH B:2434 , HOH B:2458 , HOH B:2460 , HOH B:2481 , LEU C:280 , GLY C:281 , GLY C:282BINDING SITE FOR RESIDUE FMN B 2400
3AC3SOFTWARELEU B:280 , GLY B:281 , ARG C:50 , SER C:103 , HIS C:104 , ARG C:123 , SER C:125 , LEU C:240 , ASN C:241 , GLY C:242 , LYS C:296 , THR C:298 , PRO C:299 , SER C:300 , ILE C:327 , HOH C:3419BINDING SITE FOR RESIDUE FMN C 3400
4AC4SOFTWARELEU A:280 , GLY A:281 , SER D:103 , HIS D:104 , ARG D:123 , SER D:125 , LEU D:240 , ASN D:241 , GLY D:242 , LYS D:296 , THR D:298 , PRO D:299 , SER D:300 , ILE D:327 , ARG D:330 , HOH D:4414 , HOH D:4433 , HOH D:4476 , HOH D:4514BINDING SITE FOR RESIDUE FMN D 4400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UM0)

(-) PROSITE Motifs  (3, 12)

Asymmetric/Biological Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_SYNTHASE_1PS00787 Chorismate synthase signature 1.AROC_HELPY14-29
 
 
 		  4A:14-29
B:14-29
C:14-29
D:14-29
2CHORISMATE_SYNTHASE_2PS00788 Chorismate synthase signature 2.AROC_HELPY122-138
 
 
 		  4A:122-138
B:122-138
C:122-138
D:122-138
3CHORISMATE_SYNTHASE_3PS00789 Chorismate synthase signature 3.AROC_HELPY322-338
 
 
 		  4A:322-338
B:322-338
C:322-338
D:322-338

(-) Exons   (0, 0)

(no "Exon" information available for 1UM0)

(-) 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:365
 aligned with AROC_HELPY | P56122 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:365
                                    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     
           AROC_HELPY     1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
               SCOP domains d1um0a_ A: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeee.......eeeeeee........hhhhhhhhhhhhh.......hhhhhh.eeee...ee..ee....eeeeee....................hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..ee....hhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeeee.................hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh..ee..ee.......ee..ee....eeeeeee.........eeee.....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA--------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1um0 A   1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
                                    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     


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with AROC_HELPY | P56122 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:365
                                    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     
           AROC_HELPY     1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
               SCOP domains d1um0b_ B: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeee.......eeeeeee........hhhhhhhhhhhhh.......hhhhhh.eeee...ee..ee....eeeeee....................hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..ee....hhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeeee.................hhhhhhhhhhhh...eeeeee.hhhhhhhh.....................ee..ee....eeeeeee........eeeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA--------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1um0 B   1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
                                    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     


Chain C from PDB  Type:PROTEIN  Length:365
 aligned with AROC_HELPY | P56122 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:365
                                    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     
           AROC_HELPY     1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
               SCOP domains d1um0c_ C: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeee.......eeeeeee........hhhhhhhhhhhhhh.............eeee...ee..ee....eeeeee..............ee....hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..ee....hhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeeee.................hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...............ee..ee....eeeeeee............ee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA--------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1um0 C   1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
                                    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     


Chain D from PDB  Type:PROTEIN  Length:365
 aligned with AROC_HELPY | P56122 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:365
                                    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     
           AROC_HELPY     1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
               SCOP domains d1um0d_ D: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Chorismate_synt-1um0D01 D:8-349                                                                                                                                                                                                                                                                                                                       ---------------- Pfam domains (1)
           Pfam domains (2) -------Chorismate_synt-1um0D02 D:8-349                                                                                                                                                                                                                                                                                                                       ---------------- Pfam domains (2)
           Pfam domains (3) -------Chorismate_synt-1um0D03 D:8-349                                                                                                                                                                                                                                                                                                                       ---------------- Pfam domains (3)
           Pfam domains (4) -------Chorismate_synt-1um0D04 D:8-349                                                                                                                                                                                                                                                                                                                       ---------------- Pfam domains (4)
         Sec.struct. author ..ee....eeee.......eeeeeee........hhhhhhhhhhhh................eee...ee..ee....eeeeee....................hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..ee....hhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeeee.................hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh..ee..ee.......ee..ee....eeeeeee........eeeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA--------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1um0 D   1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKEDDKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRGGGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDEEQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGLNGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPSIFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKTIYNEN 365
                                    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
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UM0)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Chorismate_synt] (9)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AROC_HELPY | P56122)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0004107    chorismate synthase activity    Catalysis of the reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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.

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        AROC_HELPY | P56122: 1umf

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