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(-) Description

Title :  THE CRYSTAL STRUCTURE OF L-PHE INHIBITED PREPHENATE DEHYDRATASE FROM CHLOROBIUM TEPIDUM TLS
 
Authors :  K. Tan, H. Li, S. Clancy, A. Joachimiak, Midwest Center For Structur Genomics (Mcsg)
Date :  17 Jul 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Apc86053, L-Phe Inhibition, Prephenate Dehydratase, Pdt, Chlorobium Tepidum Tls, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, H. Li, R. Zhang, M. Gu, S. T. Clancy, A. Joachimiak
Structures Of Open (R) And Close (T) States Of Prephenate Dehydratase (Pdt) - Implication Of Allosteric Regulation By L-Phenylalanine.
J. Struct. Biol. V. 162 94 2008
PubMed-ID: 18171624  |  Reference-DOI: 10.1016/J.JSB.2007.11.009

(-) Compounds

Molecule 1 - PREPHENATE DEHYDRATASE
    Atcc: 49652
    Chains: A, B
    EC Number: 4.2.1.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PHEA, CT1666
    Organism Scientific: CHLOROBIUM TEPIDUM TLS
    Organism Taxid: 194439
    Strain: TLS, DSM 12025

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PHE2Mod. Amino AcidPHENYLALANINE
Biological Unit 1 (4, 21)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PHE2Mod. Amino AcidPHENYLALANINE
Biological Unit 2 (4, 42)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO22Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PHE4Mod. Amino AcidPHENYLALANINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:14 , TYR A:15 , SER A:16 , HOH A:315BINDING SITE FOR RESIDUE ACT A 301
02AC2SOFTWAREARG A:263 , GLU A:264 , ALA A:266 , EDO A:308BINDING SITE FOR RESIDUE ACT A 302
03AC3SOFTWAREASP A:224 , LEU A:225 , THR A:226 , LYS A:227 , ASN B:206 , GLU B:207 , GLY B:209 , SER B:210 , LEU B:211 , SER B:230 , TYR B:240BINDING SITE FOR RESIDUE PHE A 303
04AC4SOFTWAREASN A:206 , GLU A:207 , GLY A:209 , SER A:210 , LEU A:211 , SER A:230 , TYR A:240 , ASP B:224 , LEU B:225 , THR B:226 , LYS B:227BINDING SITE FOR RESIDUE PHE A 304
05AC5SOFTWAREARG A:195 , ASP A:224 , ASN B:206BINDING SITE FOR RESIDUE EDO A 306
06AC6SOFTWAREGLU A:152BINDING SITE FOR RESIDUE EDO A 307
07AC7SOFTWAREARG A:263 , ALA A:266 , ACT A:302BINDING SITE FOR RESIDUE EDO A 308
08AC8SOFTWAREARG B:213BINDING SITE FOR RESIDUE EDO A 309
09AC9SOFTWAREARG A:221 , GLY A:222BINDING SITE FOR RESIDUE EDO A 310
10BC1SOFTWARETHR A:40 , GLU A:41 , GLN A:42 , PRO B:280BINDING SITE FOR RESIDUE EDO A 311
11BC2SOFTWARELYS A:98BINDING SITE FOR RESIDUE EDO A 312
12BC3SOFTWARELYS B:98 , MSE B:100BINDING SITE FOR RESIDUE EDO B 281
13BC4SOFTWAREILE B:223 , ASP B:224 , ILE B:247BINDING SITE FOR RESIDUE EDO B 282
14BC5SOFTWAREARG B:263 , MSE B:268 , VAL B:269BINDING SITE FOR RESIDUE EDO B 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QMX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QMX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QMX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QMX)

(-) Exons   (0, 0)

(no "Exon" information available for 2QMX)

(-) 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:280
 aligned with Q8KBW6_CHLTE | Q8KBW6 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                                                                                                                                                                                                                                                                                               280  
                                    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       272       | -
         Q8KBW6_CHLTE     3 NWLIAYQGEPGAYSEIAALRFGEPLPCESFDDVFSAVTEQKADYAVIPIENSLGGSIHQNYDLLLRRPVVILAETFVKVEHCLLGLPGASVETATKAMSHPQALVQCHNFFATHPQIRAEAAYDTAGSAKMVAESRDKSALAIASKRAGELYGLDILKENLADEEWNITRFFCIAHENNPDISHLKVRPDVARQKTSIVFALPNEQGSLFRALATFALRGIDLTKIESRPSRKKAFEYLFYADFIGHREDQNVHNALENLREFATMVKVLGSYGVVNP--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qmxA01 A:3-81,A:168-178 Periplasmic binding protein-like II                   2qmxA02 A:82-167 Periplasmic binding protein-like II                                  2qmxA01    -----------2qmxA03 A:190-280  [code=3.30.70.260, no name defined]                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhheeeee.hhhhhhhhhhh....eeeeeeee.....hhhhhhhhhhh.eeeeeeeeee...eeee..........eeeehhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eeeeehhhhhhhh..eeee.........eeeeeeeee.............eeeeeeeeeeeeee...hhhhhhhhhhhh....eeeeeeee......eeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qmx A   3 NWLIAYQGEPGAYSEIAALRFGEPLPCESFDDVFSAVTEQKADYAVIPIENSLGGSIHQNYDLLLRRPVVILAETFVKVEHCLLGLPGASVETATKAmSHPQALVQCHNFFATHPQIRAEAAYDTAGSAKmVAESRDKSALAIASKRAGELYGLDILKENLADEEWNITRFFCIAHENNPDISHLKVRPDVARQKTSIVFALPNEQGSLFRALATFALRGIDLTKIESRPSRKKAFEYLFYADFIGHREDQNVHNALENLREFATmVKVLGSYGVVNPFF 304
                                    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     | 272       304
                                                                                                                           100-MSE                          133-MSE                                                                                                                                268-MSE     280| 
                                                                                                                                                                                                                                                                                                                303 


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with Q8KBW6_CHLTE | Q8KBW6 from UniProtKB/TrEMBL  Length:280

    Alignment length:278
                                    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       272        
         Q8KBW6_CHLTE     3 NWLIAYQGEPGAYSEIAALRFGEPLPCESFDDVFSAVTEQKADYAVIPIENSLGGSIHQNYDLLLRRPVVILAETFVKVEHCLLGLPGASVETATKAMSHPQALVQCHNFFATHPQIRAEAAYDTAGSAKMVAESRDKSALAIASKRAGELYGLDILKENLADEEWNITRFFCIAHENNPDISHLKVRPDVARQKTSIVFALPNEQGSLFRALATFALRGIDLTKIESRPSRKKAFEYLFYADFIGHREDQNVHNALENLREFATMVKVLGSYGVVNP 280
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qmxB01 B:3-81,B:168-178 Periplasmic binding protein-like II                   2qmxB02 B:82-167 Periplasmic binding protein-like II                                  2qmxB01    -----------2qmxB03 B:190-280  [code=3.30.70.260, no name defined]                                      CATH domains
           Pfam domains (1) ---PDT-2qmxB03 B:6-181                                                                                                                                                             ----------------ACT-2qmxB01 B:198-265                                               --------------- Pfam domains (1)
           Pfam domains (2) ---PDT-2qmxB04 B:6-181                                                                                                                                                             ----------------ACT-2qmxB02 B:198-265                                               --------------- Pfam domains (2)
         Sec.struct. author ..eeeee....hhhhhhhh...eeeee.hhhhhhhhhh.....eeeeeeee.....hhhhhhhhhhh.eeeeeeeeee...eeee..........eeeehhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh...eeeeehhhhhhhh..eeeee........eeeeeeeee.............eeeeeeeeeeeeee...hhhhhhhhhhhh....eeeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qmx B   3 NWLIAYQGEPGAYSEIAALRFGEPLPCESFDDVFSAVTEQKADYAVIPIENSLGGSIHQNYDLLLRRPVVILAETFVKVEHCLLGLPGASVETATKAmSHPQALVQCHNFFATHPQIRAEAAYDTAGSAKmVAESRDKSALAIASKRAGELYGLDILKENLADEEWNITRFFCIAHENNPDISHLKVRPDVARQKTSIVFALPNEQGSLFRALATFALRGIDLTKIESRPSRKKAFEYLFYADFIGHREDQNVHNALENLREFATmVKVLGSYGVVNP 280
                                    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     | 272        
                                                                                                                           100-MSE                          133-MSE                                                                                                                                268-MSE
   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 2QMX)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: ACT (34)
(-)
Family: ACT (19)
(-)
Chlorobium tepidum (1)
1aACT-2qmxB01B:198-265
1bACT-2qmxB02B:198-265
(-)
Clan: no clan defined [family: PDT] (2)
(-)
Family: PDT (2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8KBW6_CHLTE | Q8KBW6)
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: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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