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(-) Description

Title :  CRYSTAL STRUCTURE OF A SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE WITH SURFACE MUTATION V3I FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH FK506
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Dec 11  (Deposition) - 18 Jan 12  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Ssgcid, Isomerase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Protein Binding, Protein Binding- Inhibitor Complex (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 - UBIQUITIN-LIKE PROTEIN SMT3,PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
    Chains: A
    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
    Fragment: Q12306 RESIDUES 13-99, Q3JK38 RESIDUES 2-113
    Gene: SMT3, YDR510W, D9719.15, BURPS1710B_A0907
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C), BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 559292, 320372
    Other Details: FUSION PROTEIN
    Strain: ATCC 204508 / S288C, 1710B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FK51Ligand/Ion8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:33 , PHE A:43 , ASP A:44 , ARG A:49 , PHE A:53 , MET A:61 , VAL A:62 , ILE A:63 , TRP A:66 , GLY A:88 , TYR A:89 , ARG A:92 , ILE A:98 , PHE A:106 , HOH A:136 , HOH A:176BINDING SITE FOR RESIDUE FK5 A 114

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SMT3_YEAST22-98  1A:-76-0

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR510W1YDR510W.1IV:1469393-1469698306SMT3_YEAST1-1011011A:-77-3 (gaps)81

(-) 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:185
 aligned with Q3JK38_BURP1 | Q3JK38 from UniProtKB/TrEMBL  Length:113

    Alignment length:185
                                                                                                    1                                                                                                                
                                     -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108     
         Q3JK38_BURP1     - ------------------------------------------------------------------------MTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....hhhhhhhhhhhh.eeee..ee...............eeeeee........eee.....eeeeee...........eeeeeeeeee....eeee.hhhh..eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vaw A -77 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTIVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                   -68       -58       -48     ||-32       -22       -12        -2         8        18        28        38        48        58        68        78        88        98       108     
                                                             -42|                                                                                                                                                    
                                                              -35                                                                                                                                                    


Chain A from PDB  Type:PROTEIN  Length:185
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:191
                                                                                                          101                                                                                                              
                                    30        40        50        60        70        80        90       100|        -         -         -         -         -         -         -         -         -         -         - 
           SMT3_YEAST    21 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGATY--------------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....hhhhhhhhhhhh------.eeee..ee...............eeeeee........eee.....eeeeee...........eeeeeeeeee....eeee.hhhh..eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN_2  PDB: A:-76-0 UniProt: 22-98                                     ----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:-77-3 (gaps) UniProt: 1-101 [INCOMPLETE]                        -------------------------------------------------------------------------------------------------------------- Transcript 1
                 3vaw A -77 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQ------LRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTIVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                   -68       -58       -48     |   -  |    -28       -18        -8         2        12        22        32        42        52        62        72        82        92       102       112 
                                                             -42    -35
   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 3VAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMT3_YEAST | Q12306)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005940    septin ring    A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

Chain A   (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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  3vaw
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  SMT3_YEAST | Q12306
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3JK38_BURP1 | Q3JK38: 3uqa 5klx
        SMT3_YEAST | Q12306: 1euv 1l2n 2eke 3pge 3qht 3tix 3uf8 3uqa 3uqb 3v60 3v61 3v62 4fn2 4g50 4ggq 4giv 5d6j 5jne 5klx
UniProtKB/TrEMBL
        Q3JK38_BURP1 | Q3JK38: 2l2s 3uf8 3uqb 4dz2 4dz3 4fn2 4g50 4ggq 4giv

(-) Related Entries Specified in the PDB File

2keo 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: TARGETDB
2ko7
2l2s
3uf8
3uqa
3uqb
4dz2
4dz3
4fn2
4g50
4ggq
4giv