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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF SURA FRAGMENT LACKING THE SECOND PEPTIDYL-PROLYL ISOMERASE DOMAIN COMPLEXED WITH PEPTIDE NFTLKFWDIFRK
 
Authors :  X. Xu, D. B. Mckay
Date :  09 May 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Survival Protein A, Peptidyl-Prolyl Cis-Trans Isomerase Domain, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xu, S. Wang, Y. X. Hu, D. B. Mckay
The Periplasmic Bacterial Molecular Chaperone Sura Adapts Its Structure To Bind Peptides In Different Conformations T Assert A Sequence Preference For Aromatic Residues.
J. Mol. Biol. V. 373 367 2007
PubMed-ID: 17825319  |  Reference-DOI: 10.1016/J.JMB.2007.07.069
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHAPERONE SURA
    Chains: A, B
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SURVIVIAL PROTEIN A FRAGMENT FROM WHICH THE SECOND PEPTIDYL-PROLYL ISOMERASE DOMAIN HAS BEEN DELETED
    Gene: SURA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K-12 EMG2
    Synonym: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SURA, PPIASE SURA, ROTAMASE SURA, SURVIVAL PROTEIN A
 
Molecule 2 - C-PEPTIDE
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PV3)

(-) Sites  (0, 0)

(no "Site" information available for 2PV3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PV3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:257 -Pro A:258
2Gly B:257 -Pro B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PV3)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPIC_PPIASE_2PS50198 PpiC-type peptidyl-prolyl cis-trans isomerase family profile.SURA_ECOLI171-272
 
282-382		  2A:171-272
B:171-272
-
2PPIC_PPIASE_1PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature.SURA_ECOLI212-232
 
321-342		  2A:212-232
B:212-232
-

(-) Exons   (0, 0)

(no "Exon" information available for 2PV3)

(-) 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:284
 aligned with SURA_ECOLI | P0ABZ6 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:403
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
           SURA_ECOLI    25 VDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAAAAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELLDTRNVDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILS 427
               SCOP domains d2pv3a1 A:25-163,A:396-427 Porin chaperone SurA, peptide-binding domain                                                                    --------d2pv3a2 A:172-273 Porin chaperone Sur  A, PPIase domains                                                                                                                                                                   -----d2pv3a1 A:25-163,A:396-427       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh.--hhhhhhhh...........eeeee.....hhhhhhhhh......eeeeeee..eeeeeee...---------------------------------------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------PPIC_PPIASE_2  PDB: A:171-272 UniProt: 171-272                                                        ---------PPIC_PPIASE_2  PDB: - UniProt: 282-382                                                               --------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PPIC_PPIASE_1        ----------------------------------------------------------------------------------------PPIC_PPIASE_1  PDB: - ------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pv3 A  25 VDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARN--DFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDL---------------------------------------------------------------------------------------------------------------------AAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILS 427
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204   |  |214       224       234       244       254       264        |-         -         -         -         -         -         -         -         -         -         -         -      |394       404       414       424   
                                                                                                                                                                                                                 208  |                                                           273                                                                                                                   391                                    
                                                                                                                                                                                                                    211                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with SURA_ECOLI | P0ABZ6 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:403
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
           SURA_ECOLI    25 VDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAAAAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELLDTRNVDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILS 427
               SCOP domains d2pv3b1 B:25-163,B:396-427 Porin chaperone SurA, peptide-binding domain                                                                    --------d2pv3b2 B:172-273 Porin chaperone Sur  A, PPIase domains                                                                                                                                                                   -----d2pv3b1 B:25-163,B:396-427       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SurA_N-2pv3B03 B:25-142                                                                                               -----------------------------------Rotamase-2pv3B01 B:178-272                                                                     -                                                                                                                     ------------------------------------- Pfam domains (1)
           Pfam domains (2) SurA_N-2pv3B04 B:25-142                                                                                               -----------------------------------Rotamase-2pv3B02 B:178-272                                                                     -                                                                                                                     ------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee...eeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeee..eeee.....hhhhhhhhhhhhhhhhhhhh.--.hhhhhhhhh..hhhhhh...eeee....hhhhhh.........eeeeee...eeeeeeeee.---------------------------------------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------PPIC_PPIASE_2  PDB: B:171-272 UniProt: 171-272                                                        ---------PPIC_PPIASE_2  PDB: - UniProt: 282-382                                                               --------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PPIC_PPIASE_1        ----------------------------------------------------------------------------------------PPIC_PPIASE_1  PDB: - ------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pv3 B  25 VDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARN--DFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDL---------------------------------------------------------------------------------------------------------------------AAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILS 427
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204   |  |214       224       234       244       254       264        |-         -         -         -         -         -         -         -         -         -         -         -      |394       404       414       424   
                                                                                                                                                                                                                 208  |                                                           273                                                                                                                   391                                    
                                                                                                                                                                                                                    211                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2pv3 C   1 NFTLKFWDIF  10
                                    10
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PV3)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: FKBP (43)
(-)
Clan: Trigger_C (7)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SURA_ECOLI | P0ABZ6)
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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0043165    Gram-negative-bacterium-type cell outer membrane assembly    The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0051085    chaperone mediated protein folding requiring cofactor    The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0060274    maintenance of stationary phase    The homeostatic process in which a population of cells changes its metabolic activity resulting in the rate of death in the population equaling the rate of reproduction. Stationary phase can be in response to limited nutrients or a build-up of toxic substances in the environment.
    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.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0044010    single-species biofilm formation    A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  Cis Peptide Bonds
    Gly A:257 - Pro A:258   [ RasMol ]  
    Gly B:257 - Pro B:258   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SURA_ECOLI | P0ABZ6: 1m5y 2pv1 2pv2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PV3)