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(-) Description

Title :  ARG90CIT CHORISMATE MUTASE OF BACILLUS SUBTILIS IN COMPLEX WITH A TRANSITION STATE ANALOG
 
Authors :  D. Burschowsky, A. Vaneerde, M. Okvist, A. Kienhofer, P. Kast, D. Hilve U. Krengel
Date :  26 Feb 13  (Deposition) - 16 Apr 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Pseudo-Alpha Beta-Barrel, Isomerase, Non-Proteinogenic Amino Acid, Semi-Synthetic, Transition State Analog (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Burschowsky, A. Van Eerde, M. Okvist, A. Kienhofer, P. Kast, D. Hilvert, U. Krengel
Electrostatic Transition State Stabilization Rather Than Reactant Destabilization Provides The Chemical Basis For Efficient Chorismate Mutase Catalysis.
Proc. Natl. Acad. Sci. Usa V. 111 17516 2014
PubMed-ID: 25422475  |  Reference-DOI: 10.1073/PNAS.1408512111

(-) Compounds

Molecule 1 - CHORISMATE MUTASE AROH
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: CHORISMATE MUTASE, CM

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CIR6Mod. Amino AcidCITRULLINE
2TSA4Ligand/Ion8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CIR3Mod. Amino AcidCITRULLINE
2TSA2Ligand/Ion8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CIR3Mod. Amino AcidCITRULLINE
2TSA2Ligand/Ion8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:7 , GLU A:78 , CIR A:90 , TYR A:108 , PHE C:57 , ALA C:59 , ARG C:63 , VAL C:73 , THR C:74 , CYS C:75BINDING SITE FOR RESIDUE TSA C1118
2AC2SOFTWAREPHE B:57 , ALA B:59 , LYS B:60 , VAL B:73 , THR B:74 , CYS B:75 , HOH B:2036 , ARG C:7 , GLU C:78 , CIR C:90 , TYR C:108 , LEU C:115BINDING SITE FOR RESIDUE TSA B1118
3AC3SOFTWAREARG D:7 , GLU D:78 , CIR D:90 , TYR D:108 , LEU D:115 , PHE F:57 , ALA F:59 , LYS F:60 , VAL F:73 , THR F:74 , CYS F:75BINDING SITE FOR RESIDUE TSA F1118
4AC4SOFTWAREPHE D:57 , ALA D:59 , LYS D:60 , ARG D:63 , VAL D:73 , THR D:74 , CYS D:75 , ARG E:7 , GLU E:78 , CIR E:90 , TYR E:108 , LEU E:115BINDING SITE FOR RESIDUE TSA D1118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZP4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZP4)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_MUT_1PS51167 Chorismate mutase domain profile.AROH_BACSU3-121
 
 
 
 
 		  6A:3-117
B:3-117
C:3-117
D:3-117
E:3-117
F:3-117
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_MUT_1PS51167 Chorismate mutase domain profile.AROH_BACSU3-121
 
 
 
 
 		  3A:3-117
B:3-117
C:3-117
-
-
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_MUT_1PS51167 Chorismate mutase domain profile.AROH_BACSU3-121
 
 
 
 
 		  3-
-
-
D:3-117
E:3-117
F:3-117

(-) Exons   (0, 0)

(no "Exon" information available for 3ZP4)

(-) Sequences/Alignments

Asymmetric 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:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeeee..hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: A:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 A   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR                       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: B:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 B   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR                       


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: C:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 C   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR                       


Chain D from PDB  Type:PROTEIN  Length:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeeee..hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: D:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 D   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR                       


Chain E from PDB  Type:PROTEIN  Length:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: E:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 E   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR                       


Chain F from PDB  Type:PROTEIN  Length:117
 aligned with AROH_BACSU | P19080 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_BACSU     1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRP 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhh.......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_1  PDB: F:3-117 UniProt: 3-121                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp4 F   1 MMIRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVRELSGWQYVPVTCMQEMDVTGGLKKCIrVMMTVQTDVPQEQIRHVYLEKAVVLRP 117
                                    10        20        30        40        50        60        70        80        90       100       110       
                                                                                                                    90-CIR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3ZP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZP4)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (AROH_BACSU | P19080)
molecular function
    GO:0004106    chorismate mutase activity    Catalysis of the reaction: chorismate = prephenate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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:0046417    chorismate metabolic process    The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3zp4
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROH_BACSU | P19080: 1com 1dbf 1fnj 1fnk 2chs 2cht 3zo8 3zop 3zp7

(-) Related Entries Specified in the PDB File

3zo8 WILD-TYPE CHORISMATE MUTASE OF BACILLUS SUBTILIS AT 1.6 A RESOLUTION
3zop ARG90CIT CHORISMATE MUTASE OF BACILLUS SUBTILIS AT 1.6 A RESOLUTION
3zp8 ARG90CIT CHORISMATE MUTASE OF BACILLUS SUBTILIS IN COMPLEX WITH CHORISMATE AND PREPHENATE