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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CYCLOHEXADIENYL DEHYDRATASE PRECURSOR FROM PSEUDOMONAS AERUGINOSA PA01
 
Authors :  K. Tan, N. Marshall, K. Buck, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  20 Oct 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Cyclohexadienyl Dehydratase Precursor, Pseudomonas Aeruginosa Pa01, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Amino-Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Lyase, Multifunctional Enzyme, Phenylalanine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, N. Marshall, K. Buck, A. Joachimiak
The Crystal Structure Of Cyclohexadienyl Dehydratase Precursor From Pseudomonas Aeruginosa Pa01
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYCLOHEXADIENYL DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.51, 4.2.1.91
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG9
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA3475, PHEC, PSEUDOMONAS AERUGINOSA
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PA01
    Synonym: PREPHENATE DEHYDRATASE, AROGENATE DEHYDRATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FMT2Ligand/IonFORMIC ACID
4GOL5Ligand/IonGLYCEROL
5MSE6Mod. Amino AcidSELENOMETHIONINE
6NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (4, 84)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FMT12Ligand/IonFORMIC ACID
4GOL30Ligand/IonGLYCEROL
5MSE36Mod. Amino AcidSELENOMETHIONINE
6NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:134 , HIS A:213 , HIS A:256 , CL A:262 , HOH A:394BINDING SITE FOR RESIDUE NI A 1
02AC2SOFTWARENI A:1 , GLU A:134 , CYS A:210 , HIS A:213 , HIS A:256 , HOH A:412BINDING SITE FOR RESIDUE CL A 262
03AC3SOFTWAREASP A:219 , ALA A:221 , HOH A:324 , HOH A:359BINDING SITE FOR RESIDUE GOL A 263
04AC4SOFTWAREGLU A:27 , ASP A:31 , ARG A:32 , GLU A:35BINDING SITE FOR RESIDUE GOL A 2
05AC5SOFTWAREGLU A:27 , SER A:28 , ASP A:230 , GLU A:231 , ALA A:232BINDING SITE FOR RESIDUE GOL A 3
06AC6SOFTWARELEU A:34 , GLU A:35 , SER A:36 , GLY A:37 , GLY A:75 , HOH A:327BINDING SITE FOR RESIDUE GOL A 4
07AC7SOFTWARELEU A:172 , VAL A:173 , HIS A:174 , PRO A:175BINDING SITE FOR RESIDUE GOL A 5
08AC8SOFTWAREMSE A:254 , GLU A:255BINDING SITE FOR RESIDUE FMT A 264
09AC9SOFTWAREPRO A:214 , GLN A:215 , PRO A:217 , HOH A:336BINDING SITE FOR RESIDUE FMT A 265
10BC1SOFTWAREHOH A:18 , ASP A:46 , TRP A:85 , GLY A:103 , ILE A:104 , SER A:105 , ARG A:110 , THR A:157 , ASN A:177 , ASP A:195 , GLU A:198 , LYS A:223 , HOH A:279 , HOH A:297BINDING SITE FOR RESIDUE EPE A 266

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:131 -A:210

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:48 -Pro A:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_3PS01039 Bacterial extracellular solute-binding proteins, family 3 signature.PHEC_PSEAE61-74  1A:61-74
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_3PS01039 Bacterial extracellular solute-binding proteins, family 3 signature.PHEC_PSEAE61-74  6A:61-74

(-) Exons   (0, 0)

(no "Exon" information available for 3KBR)

(-) 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:231
 aligned with PHEC_PSEAE | Q01269 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:232
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
           PHEC_PSEAE    27 ESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDEAFKRYVDQWLHIAEQSGLLRQRMEHWL 258
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------SBP_bac_3-3kbrA01 A:39-258                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .hhhhhhhhhheeeeee..ee...eee.....eehhhhhhhhhhhhhh..eeeeee....hhhhhhhh....ee......hhhhhh..ee....eee.eeeeee.hhhhhhhhhhhhh....eeee...hhhhhhhhhhh...eeee.....hhhhhhhh....eeeeehhhhhhhhhhh..eee....-....eee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SBP_BACTERIAL_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kbr A  27 ESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDmAQRLAESLGAKLVVVPTSWPNLmRDFADDRFDIAmSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLmmTDAIEARLQSRLHPELCAVHPQ-PFDFAEKAYLLPRDEAFKRYVDQWLHIAEQSGLLRQRmEHWL 258
                                    36        46        56        66        76        86  |     96    |  106       116       126       136       146       156       166       176       186     ||196       206        |-|      226       236       246       256  
                                                                  66-MSE                 89-MSE     101-MSE                                                                                    192-MSE                215 |                                  254-MSE
                                                                                                                                                                                                193-MSE                 217
   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 3KBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHEC_PSEAE | Q01269)
molecular function
    GO:0047769    arogenate dehydratase activity    Catalysis of the reaction: L-arogenate = L-phenylalanine + H2O + CO2.
    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: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.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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        PHEC_PSEAE | Q01269: 5hpq 5jot

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