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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PREPHENATE DEHYDRATASE IN COMPLEX WITH L-PHE FROM ARTHROBACTER AURESCENS TO 2.0A
 
Authors :  A. J. Stein, G. Chhor, K. Buck, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  05 May 10  (Deposition) - 30 Jun 10  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  L-Phe, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, G. Chhor, K. Buck, A. Joachimiak
The Crystal Structure Of Prephenate Dehydratase In Complex With L-Phe From Arthrobacter Aurescens To 2. 0A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PREPHENATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHEA, AAUR_0101
    Organism Scientific: ARTHROBACTER AURESCENS
    Organism Taxid: 290340
    Strain: TC1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PHE2Mod. Amino AcidPHENYLALANINE
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
3PHE4Mod. Amino AcidPHENYLALANINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PHE2Mod. Amino AcidPHENYLALANINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:226 , LEU A:227 , SER A:228 , ARG A:229 , ILE A:230 , HOH A:442 , ASP B:208 , HIS B:209 , GLY B:211 , ALA B:212 , LEU B:213 , PHE B:244 , HOH B:447BINDING SITE FOR RESIDUE PHE B 311
2AC2SOFTWAREASP A:208 , HIS A:209 , GLY A:211 , ALA A:212 , LEU A:213 , SER A:232 , PHE A:244 , ASN B:226 , LEU B:227 , SER B:228 , ARG B:229 , ILE B:230 , HOH B:438 , HOH B:439BINDING SITE FOR RESIDUE PHE B 312
3AC3SOFTWAREALA B:158 , GLN B:161 , LEU B:164BINDING SITE FOR RESIDUE MG B 313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:10 -Pro A:11
2Gly B:10 -Pro B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MWB)

(-) Exons   (0, 0)

(no "Exon" information available for 3MWB)

(-) 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:306
 aligned with A1R118_PAEAT | A1R118 from UniProtKB/TrEMBL  Length:310

    Alignment length:306
                                    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       273       283       293       303      
         A1R118_PAEAT     4 VTYTFLGPQGTFTEAALMQVPGAADATRIPCTNVNTALERVRAGEADAAMVPIENSVEGGVTATLDAIATGQELRIIREALVPITFVLVARPGVELSDIKRISTHGHAWAQCRLWVDEHLPNADYVPGSSTAASAMGLLEDDAPYEAAICAPLIAAEQPGLNVLAEDIGDNPDAVTRFILVSRPGALPERTGADKTTVVVPLPEDHPGALMEILDQFASRGVNLSRIESRPTGQYLGHYFFSIDADGHATDSRVADALAGLHRISPATRFLGSYARADKQPAVVAPHTSDAAFASAHAWVDSILKG 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhh...hhhhheeeee.hhhhhhhhhhh....eeeeeee.....hhhhhhhhh......eeeeeeeee...eeee....hhhhh.eeeehhhhhh.hhhhhhhhh...eeee..hhhhhhhhh........eeeehhhhhhhh...eeee.........eeeeeeee...........eeeeeeee......hhhhhhhhhhhh....eeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhh...eeeeeee.............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mwb A   4 VTYTFLGPQGTFTEAALmQVPGAADATRIPCTNVNTALERVRAGEADAAmVPIENSVEGGVTATLDAIATGQELRIIREALVPITFVLVARPGVELSDIKRISTHGHAWAQCRLWVDEHLPNADYVPGSSTAASAmGLLEDDAPYEAAICAPLIAAEQPGLNVLAEDIGDNPDAVTRFILVSRPGALPERTGADKTTVVVPLPEDHPGALmEILDQFASRGVNLSRIESRPTGQYLGHYFFSIDADGHATDSRVADALAGLHRISPATRFLGSYARADKQPAVVAPHTSDAAFASAHAWVDSILKG 309
                                    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       273       283       293       303      
                                            21-MSE                          53-MSE                                                                               139-MSE                                                                    214-MSE                                                                                           


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with A1R118_PAEAT | A1R118 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                                                                                                                                                                                                                                                                                                                            310  
                                    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       273       283       293       303      |  
         A1R118_PAEAT     4 VTYTFLGPQGTFTEAALMQVPGAADATRIPCTNVNTALERVRAGEADAAMVPIENSVEGGVTATLDAIATGQELRIIREALVPITFVLVARPGVELSDIKRISTHGHAWAQCRLWVDEHLPNADYVPGSSTAASAMGLLEDDAPYEAAICAPLIAAEQPGLNVLAEDIGDNPDAVTRFILVSRPGALPERTGADKTTVVVPLPEDHPGALMEILDQFASRGVNLSRIESRPTGQYLGHYFFSIDADGHATDSRVADALAGLHRISPATRFLGSYARADKQPAVVAPHTSDAAFASAHAWVDSILKGS--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhh.......eeeee.hhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh...eeeeeeeee...eeee....hhhhh.eeeeehhhhhhhhhhhhhhh...eeeee.hhhhhhhhh........eeeehhhhhhhh...eeeee........eeeeeeee...........eeeeeeee......hhhhhhhhhhhh....eeeeeeee.---...eeeeeeee....hhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhh.-.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mwb B   4 VTYTFLGPQGTFTEAALmQVPGAADATRIPCTNVNTALERVRAGEADAAmVPIENSVEGGVTATLDAIATGQELRIIREALVPITFVLVARPGVELSDIKRISTHGHAWAQCRLWVDEHLPNADYVPGSSTAASAmGLLEDDAPYEAAICAPLIAAEQPGLNVLAEDIGDNPDAVTRFILVSRPGALPERTGADKTTVVVPLPEDHPGALmEILDQFASRGVNLSRIESRPT---LGHYFFSIDADGHATDSRVADALAGLHRISPATRFLGSYARADKQPAVVAPHTSDAAFASAHAWVDSILKG-FF 312
                                    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       273       283       293       303     | | 
                                            21-MSE                          53-MSE                                                                               139-MSE                                                                    214-MSE              235 239                                                                   309 | 
                                                                                                                                                                                                                                                                                                                                             311
   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 3MWB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1R118_PAEAT | A1R118)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0004106    chorismate mutase activity    Catalysis of the reaction: chorismate = prephenate.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004664    prephenate dehydratase activity    Catalysis of the reaction: prephenate = phenylpyruvate + H2O + CO2.
biological process
    GO:0009094    L-phenylalanine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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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