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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOPHILIC SLYD
 
Authors :  C. Loew, P. Neumann, M. T. Stubbs, J. Balbach
Date :  06 Mar 08  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (6x)
Keywords :  Prolyl Cis Trans Isomerase, Chaperone Function, Two Domain Protein, Rotamase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Loew, P. Neumann, H. Tidow, U. Weininger, C. Haupt, B. Friedrich-Epler, C. Scholz, M. T. Stubbs, J. Balbach
Crystal Structure Determination And Functional Characterization Of The Metallochaperone Slyd From Thermus Thermophilus
J. Mol. Biol. V. 398 375 2010
PubMed-ID: 20230833  |  Reference-DOI: 10.1016/J.JMB.2010.03.014

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PET-VECTOR
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: SLYD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NI1Ligand/IonNICKEL (II) ION
3SCN6Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NI-1Ligand/IonNICKEL (II) ION
3SCN6Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 48)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2NI-1Ligand/IonNICKEL (II) ION
3SCN36Ligand/IonTHIOCYANATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:36 , ILE A:37 , TYR A:63 , GOL A:166BINDING SITE FOR RESIDUE SCN A 159
2AC2SOFTWARETYR A:29 , LEU A:30 , ASN A:35 , HIS A:147 , ALA A:148BINDING SITE FOR RESIDUE SCN A 160
3AC3SOFTWAREPRO A:38 , GLU A:60 , PRO A:65BINDING SITE FOR RESIDUE SCN A 161
4AC4SOFTWAREVAL A:133 , LYS A:134BINDING SITE FOR RESIDUE SCN A 162
5AC5SOFTWAREHIS A:145 , HIS A:147 , HIS A:149 , HIS A:153 , HIS A:155 , HIS A:157BINDING SITE FOR RESIDUE NI A 164
6AC6SOFTWAREARG A:47BINDING SITE FOR RESIDUE SCN A 165
7AC7SOFTWAREASP A:23 , SCN A:159 , HOH A:254BINDING SITE FOR RESIDUE GOL A 166
8AC8SOFTWAREARG A:34 , ASN A:35 , LEU A:36 , HOH A:244 , HOH A:262BINDING SITE FOR RESIDUE GOL A 167

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CGM)

(-) Exons   (0, 0)

(no "Exon" information available for 3CGM)

(-) 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:157
 aligned with Q5SLE7_THET8 | Q5SLE7 from UniProtKB/TrEMBL  Length:149

    Alignment length:157
                                                                                                                                                                              149        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        |-       
         Q5SLE7_THET8     1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAH--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh....hhh.eeeee.hhh..........eeeeee...eeeeeeeeeee..eeeee.........eeeeeeeeeeee.hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgm A   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHH 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3CGM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SLE7_THET8 | Q5SLE7)
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

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        Q5SLE7_THET8 | Q5SLE7: 3cgn 3luo 4odk 4odl 4odm 4odn 4odo 4odp 4odq 4odr

(-) Related Entries Specified in the PDB File

3cgn