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(-) Description

Title :  CRYSTAL STRUCTURE OF A SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE WITH SURFACE MUTATION D44G FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH CJ183
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Aug 12  (Deposition) - 05 Sep 12  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ssgcid, Isomerase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Protein Binding (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, 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
    Fragment: Q12306 RESIDUES 13-98, Q3JK38 RESIDUES 2-113
    Gene: BURPS1710B_A0907, SMT3, YDR510W, D9719.15
    Mutation: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE, BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 559292, 320372
    Strain: 1710B, S288C

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
14GI2Ligand/Ion3-(PYRIDIN-3-YL)PROPYL (2S)-1-[(3-NITROPHENYL)SULFONYL]PIPERIDINE-2-CARBOXYLATE
2FMT2Ligand/IonFORMIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
14GI1Ligand/Ion3-(PYRIDIN-3-YL)PROPYL (2S)-1-[(3-NITROPHENYL)SULFONYL]PIPERIDINE-2-CARBOXYLATE
2FMT2Ligand/IonFORMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14GI1Ligand/Ion3-(PYRIDIN-3-YL)PROPYL (2S)-1-[(3-NITROPHENYL)SULFONYL]PIPERIDINE-2-CARBOXYLATE
2FMT-1Ligand/IonFORMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:33 , PHE A:43 , VAL A:62 , TRP A:66 , TYR A:89 , PHE A:106 , 4GI B:300BINDING SITE FOR RESIDUE 4GI A 201
2AC2SOFTWAREARG A:-52 , ALA A:-24 , ILE A:-28 , PRO A:-54 , ARG A:-27 , ASP A:-23 , HOH A:359BINDING SITE FOR RESIDUE FMT A 202
3AC3SOFTWAREARG A:-5 , LEU A:15 , THR A:16BINDING SITE FOR RESIDUE FMT A 203
4AC4SOFTWARE4GI A:201 , TYR B:33 , PHE B:43 , VAL B:62 , TRP B:66 , TYR B:89 , PHE B:106BINDING SITE FOR RESIDUE 4GI B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GIV)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....eeeeeee....hhhhhhhhhhhh..hhhhheeee..ee...............eeeeee.........ee.....eeeeee...........eeeeeeeeee....eeee.hhhh..eeee......hhhhhhhhh......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4giv A -78 PETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFGSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                   -69       -59       -49       -39       -29       -19        -9         1        11        21        31        41        51        61        71        81        91       101       111  


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee.................eeeee.....eee.....eeeeee.........eeeeeeeeee....eeee.......eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4giv B -76 THINLKVSDSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQGSTVVTTESGLKYEDLTEGSEARAGQTVSVHYTGWLTDGQKFGSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV 113
                                   -65       -55       -45       -35       -25       -15        -5 ||      7        17 ||     29        39        49        59        69        79        89        99       109    
                                  -68|                                                            -3|                 19|                                                                                           
                                   -65                                                              0                  22
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  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 4GIV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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  4giv
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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 3vaw 4fn2 4g50 4ggq 5d6j 5jne 5klx
UniProtKB/TrEMBL
        Q3JK38_BURP1 | Q3JK38: 2l2s 3uf8 3uqb 3vaw 4dz2 4dz3 4fn2 4g50 4ggq

(-) Related Entries Specified in the PDB File

2keo
2ko7
2l2s
3uf8
3uqa
3uqb
3vaw
4dz2
4dz3
4fn2
4g50
4ggq RELATED ID: SSGCID-BUPSA.00130.A RELATED DB: TARGETTRACK