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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PREPHENATE DEHYDRATASE (PDT) FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50
 
Authors :  K. Tan, R. Zhang, H. Li, M. Gu, A. Joachimiak, Midwest Center For Stru 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  (2x)
Keywords :  Apc85812, Prephenate Dehydratase (Pdt), Staphylococcus Aureus Subsp. Aureus Mu50, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (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: 700699
    Chains: A, B
    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: SAV1915
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158878
    Strain: MU50
    Synonym: PDT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MSE20Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:84 , PRO A:164 , HOH A:363 , HOH A:383 , HOH A:389BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWARETYR A:122 , ASP A:123BINDING SITE FOR RESIDUE ACT A 311
3AC3SOFTWARESER A:56 , ILE A:57 , THR A:168 , HOH A:337BINDING SITE FOR RESIDUE EDO A 321
4AC4SOFTWARETHR A:206 , LEU A:209 , SER B:202 , THR B:206BINDING SITE FOR RESIDUE EDO B 322
5AC5SOFTWARELEU A:6 , SER A:32 , ASN A:33 , LEU A:34BINDING SITE FOR RESIDUE PEG A 331

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:7 -Pro A:8
2Gly B:7 -Pro B:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QMW)

(-) 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:264
 aligned with A0A0H3K044_S | A0A0H3K044 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         A0A0H3K044_S     1 MQLYYLGPKGTFSYLACRQYFSENEATFQPKSNLFEVIKAVADDDTSIGVVPIENSIEGTINIVADALAQQDVFAHGEIRLDINFALYGNGTDSISDIKKVYSIAPAISQTTNYIHQHQFDYDYVDSTIQSLTKIENGVAAIAPLGSGEAYGFTPIDTHIEDYPHNVTRFLVIKNQQQFDQNATSLMFLITPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADSAITTDIKKVIAILETLDFKVEMIGAFN 264
               SCOP domains d2qmwa1 A:1-184 Prephenate dehydratase                                                                                                                                                  d2qmwa2 A:185-264 Prephenate dehydratase C-terminal domain                       SCOP domains
               CATH domains -2qmwA01 A:2-83,A:165-175 Periplasmic binding protein-like II                      2qmwA02 A:84-164 Periplasmic binding protein-like II                             2qmwA01    ---------2qmwA03 A:185-261  [code=3.30.70.260, no name defined]                       --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhh...eeeeeeeee..eeee...........eeeehhhhhhhhhhhhhhh..eeee..hhhhhhhh....eeeeee...hhhhh..eeee........eeeeeeee..........eeeeeeee.....hhhhhhhhhhhh....eeeeeeee.......eeeeeee....hhhhhhhhhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qmw A   1 mQLYYLGPKGTFSYLACRQYFSENEATFQPKSNLFEVIKAVADDDTSIGVVPIENSIEGTINIVADALAQQDVFAHGEIRLDINFALYGNGTDSISDIKKVYSIAPAISQTTNYIHQHQFDYDYVDSTIQSLTKIENGVAAIAPLGSGEAYGFTPIDTHIEDYPHNVTRFLVIKNQQQFDQNATSLmFLITPmHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGmYRFFVQADSAITTDIKKVIAILETLDFKVEmIGAFN 264
                            |       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    
                            |                                                                                                                                                                                       187-MSE |                                228-MSE                        259-MSE 
                            1-MSE                                                                                                                                                                                         193-MSE                                                                   


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with A0A0H3K044_S | A0A0H3K044 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         A0A0H3K044_S     1 MQLYYLGPKGTFSYLACRQYFSENEATFQPKSNLFEVIKAVADDDTSIGVVPIENSIEGTINIVADALAQQDVFAHGEIRLDINFALYGNGTDSISDIKKVYSIAPAISQTTNYIHQHQFDYDYVDSTIQSLTKIENGVAAIAPLGSGEAYGFTPIDTHIEDYPHNVTRFLVIKNQQQFDQNATSLMFLITPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADSAITTDIKKVIAILETLDFKVEMIGAFN 264
               SCOP domains d2qmwb1 B:1-184 Prephe   nate dehydratase                                                                                                                                               d2qmwb2 B:185-264 Prephenate dehydrat     ase C-terminal domain                  SCOP domains
               CATH domains -2qmwB01 B:2-83,B:165-   175 Periplasmic b  inding protei   n-like II              2qmwB02 B:84-164 Periplasmic binding protein-like II                             2qmwB01    ----  ---2qmwB03 B:185-261  [code=3.30.70.260,      no name defined]                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh---.eeeee.hhhhhhhhhh--...eeeeeee...---hhhhhhhhhh...eeeeeeeee..eeee.....hhhhh.eeeehhhhhhhhhhhhhhh..eeee..hhhhhhhhh...eeeeee..........eeee........eeeeeeee.....--...eeeeeeee.....hhhhhhhhhhhhh...eeeeeee.-----...eeeeee....hhhhhhhhhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qmw B   1 mQLYYLGPKGTFSYLACRQYFS---ATFQPKSNLFEVIKAVA--DTSIGVVPIENSI---INIVADALAQQDVFAHGEIRLDINFALYGNGTDSISDIKKVYSIAPAISQTTNYIHQHQFDYDYVDSTIQSLTKIENGVAAIAPLGSGEAYGFTPIDTHIEDYPHNVTRFLVIKNQQQF--NATSLmFLITPmHDKPGLLASVLNTFALFNINLSWIESRP-----GmYRFFVQADSAITTDIKKVIAILETLDFKVEmIGAFN 264
                            |       10        20 |   |  30        40 |  |   50      |  -|       70        80        90       100       110       120       130       140       150       160       170        |- |    |190  |    200       210       220|     |230       240       250       260    
                            1-MSE               22  26              42 45          57  61                                                                                                                   179  |    |     |                         221   227|                            259-MSE 
                                                                                                                                                                                                               182    |     |                                228-MSE                                
                                                                                                                                                                                                                    187-MSE |                                                                       
                                                                                                                                                                                                                          193-MSE
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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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QMW)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2QMW)

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