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(-) Description

Title :  CRYSTAL STRUCTURE OF A PEPTIDYL-PROLYL CIS-TRANS ISOMERASE WITH SURFACE MUTATION M61H FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH FK506
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Feb 12  (Deposition) - 28 Mar 12  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Isomerase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Begley, D. Fox, D. Jenner, C. Juli, P. G. Pierce, J. Abendroth, M. Muruthi, K. Safford, V. Anderson, K. Atkins, S. R. Barnes, S. O. Moen A. C. Raymond, R. Stacy, P. J. Myler, B. L. Staker, N. J. Harmer, I. H. Norville, U. Holzgrabe, M. Sarkar-Tyson, T. E. Edwards, D. D. Lorimer
A Structural Biology Approach Enables The Development Of Antimicrobials Targeting Bacterial Immunophilins.
Antimicrob. Agents Chemother. V. 58 1458 2014
PubMed-ID: 24366729  |  Reference-DOI: 10.1128/AAC.01875-13

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
    Chains: A, B
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-HISSMT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BURPS1710B_A0907
    Mutation: YES
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B_A0907

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4FK52Ligand/Ion8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:33 , PHE A:43 , ASP A:44 , PHE A:53 , HIS A:61 , VAL A:62 , ILE A:63 , TRP A:66 , GLY A:88 , TYR A:89 , PHE A:106 , HOH A:357 , GLY B:60 , HIS B:61 , VAL B:62 , FK5 B:201BINDING SITE FOR RESIDUE FK5 A 201
02AC2SOFTWAREASP A:112 , VAL A:113 , ASP B:51 , PRO B:52 , HOH B:321 , HOH B:333BINDING SITE FOR RESIDUE CA A 202
03AC3SOFTWARETHR A:28 , ALA B:54 , VAL B:56 , EDO B:203BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWARETHR A:2 , VAL A:4 , GLU A:13 , ASP A:14 , HOH A:353BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWARESER A:1 , THR B:6BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWARETYR A:33 , THR A:34BINDING SITE FOR RESIDUE ACT A 206
07AC7SOFTWAREGLY A:60 , HIS A:61 , VAL A:62 , FK5 A:201 , TYR B:33 , PHE B:43 , ASP B:44 , ARG B:49 , PHE B:53 , HIS B:61 , VAL B:62 , ILE B:63 , TRP B:66 , GLY B:88 , TYR B:89 , PHE B:106 , ACT B:208BINDING SITE FOR RESIDUE FK5 B 201
08AC8SOFTWAREASP A:51 , PRO A:52 , HOH A:321 , HOH A:326 , ASP B:112 , VAL B:113BINDING SITE FOR RESIDUE CA B 202
09AC9SOFTWAREVAL A:56 , EDO A:203 , THR B:28BINDING SITE FOR RESIDUE EDO B 203
10BC1SOFTWARETHR B:2 , GLU B:13 , ASP B:14BINDING SITE FOR RESIDUE EDO B 204
11BC2SOFTWARESER A:30 , ASP A:112 , HOH A:341 , SER B:30 , PRO B:52 , ASP B:112BINDING SITE FOR RESIDUE EDO B 205
12BC3SOFTWAREHIS B:32 , THR B:34BINDING SITE FOR RESIDUE ACT B 206
13BC4SOFTWARETHR B:38 , ASP B:39 , THR B:82 , VAL B:105BINDING SITE FOR RESIDUE ACT B 207
14BC5SOFTWAREGLN B:86 , GLY B:88 , GLY B:90 , FK5 B:201 , HOH B:370BINDING SITE FOR RESIDUE ACT B 208
15BC6SOFTWARELYS A:11 , HOH A:361 , THR B:5 , LYS B:11 , HOH B:344BINDING SITE FOR RESIDUE ACT B 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DZ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DZ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4DZ3)

(-) Sequences/Alignments

Asymmetric/Biological 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:113
 aligned with Q3JK38_BURP1 | Q3JK38 from UniProtKB/TrEMBL  Length:113

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
         Q3JK38_BURP1     1 MTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
               SCOP domains d4dz3a_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eeeeee...........eeeeeeeeee....eeee.......eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4dz3 A   1 STVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGHVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                    10        20        30        40        50        60        70        80        90       100       110   


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with Q3JK38_BURP1 | Q3JK38 from UniProtKB/TrEMBL  Length:113

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
         Q3JK38_BURP1     1 MTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
               SCOP domains d4dz3b_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeeee....eeee.hhhh..eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4dz3 B   1 STVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGHVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DZ3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3JK38_BURP1 | Q3JK38)
molecular function
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3JK38_BURP1 | Q3JK38: 3uqa 5klx
UniProtKB/TrEMBL
        Q3JK38_BURP1 | Q3JK38: 2l2s 3uf8 3uqb 3vaw 4dz2 4fn2 4g50 4ggq 4giv

(-) Related Entries Specified in the PDB File

2ke0
2ko7
2l2s
3uf8
3uqa
3uqb
3vaw
4dz2 SURFACE MUTATION R92G RELATED ID: 16406 RELATED DB: BMRB RELATED ID: 17151 RELATED DB: BMRB RELATED ID: 16491 RELATED DB: BMRB RELATED ID: SSGCID-BUPSA.00130.A RELATED DB: TARGETTRACK