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(-) Description

Title :  CRYSTAL STRUCTURE OF YRRB: A TPR PROTEIN WITH AN UNUSUAL PEPTIDE-BINDING SITE
 
Authors :  J. Oh, D. Han, K. Kim, H. Lim
Date :  06 Jun 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tpr, Yrrb, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Han, J. Oh, K. Kim, H. Lim, Y. Kim
Crystal Structure Of Yrrb: A Tpr Protein With An Unusual Peptide-Binding Site
Biochem. Biophys. Res. Commun. V. 360 784 2007
PubMed-ID: 17624311  |  Reference-DOI: 10.1016/J.BBRC.2007.06.129

(-) Compounds

Molecule 1 - YRRB PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A(+)
    Expression System Strain: BL21(DE3)CODON PLUS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 4-202
    Gene: YRRB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Q7F)

(-) Sites  (0, 0)

(no "Site" information available for 2Q7F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q7F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q7F)

(-) PROSITE Motifs  (1, 10)

Asymmetric Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.YRRB_BACSU1-23
24-57
 
58-91
 
92-125
 
126-159
 
160-193
 		  10-
A:58-91
B:58-91
A:92-125
B:92-125
A:126-159
B:126-159
A:160-193
B:160-193
A:194-227
B:194-227
Biological Unit 1 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.YRRB_BACSU1-23
24-57
 
58-91
 
92-125
 
126-159
 
160-193
 		  5-
A:58-91
-
A:92-125
-
A:126-159
-
A:160-193
-
A:194-227
-
Biological Unit 2 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.YRRB_BACSU1-23
24-57
 
58-91
 
92-125
 
126-159
 
160-193
 		  5-
-
B:58-91
-
B:92-125
-
B:126-159
-
B:160-193
-
B:194-227

(-) Exons   (0, 0)

(no "Exon" information available for 2Q7F)

(-) 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:194
 aligned with YRRB_BACSU | O34452 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:194
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    
           YRRB_BACSU     9 AAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL 202
               SCOP domains ------------------------------------------------------------------------------------d2q7fa1 A:127-191 automated matches                              --------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TPR  PDB: -    TPR  PDB: A:58-91 UniProt: 24-57  TPR  PDB: A:92-125 UniProt: 58-91 TPR  PDB: A:126-159               TPR  PDB: A:160-193               TPR  PDB: A:194-227               --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7f A  43 AAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL 236
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with YRRB_BACSU | O34452 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:194
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    
           YRRB_BACSU     9 AAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL 202
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TPR_11-2q7fB07 B:43-89                         -----------------------------------------------------------------------TPR_6-2q7fB11 B:161-193          TPR_1-2q7fB01 B:194-227           --------- Pfam domains (1)
           Pfam domains (2) TPR_11-2q7fB08 B:43-89                         -----------------------------------------------------------------------TPR_6-2q7fB12 B:161-193          TPR_1-2q7fB02 B:194-227           --------- Pfam domains (2)
           Pfam domains (3) TPR_2-2q7fB09  ----------------------------------------------------------------------------------------------------------------------------------------TPR_1-2q7fB03 B:194-227           --------- Pfam domains (3)
           Pfam domains (4) TPR_2-2q7fB10  ----------------------------------------------------------------------------------------------------------------------------------------TPR_1-2q7fB04 B:194-227           --------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------------------------TPR_1-2q7fB05 B:194-227           --------- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------------------------------TPR_1-2q7fB06 B:194-227           --------- Pfam domains (6)
         Sec.struct. author ....hhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TPR  PDB: -    TPR  PDB: B:58-91 UniProt: 24-57  TPR  PDB: B:92-125 UniProt: 58-91 TPR  PDB: B:126-159               TPR  PDB: B:160-193               TPR  PDB: B:194-227               --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7f B  43 AAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL 236
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q7F)

(-) Pfam Domains  (4, 12)

Asymmetric Unit
(-)
Clan: TPR (230)
(-)
Family: TPR_1 (18)
(-)
Bacillus subtilis (1)
1aTPR_1-2q7fB01B:194-227
1bTPR_1-2q7fB02B:194-227
1cTPR_1-2q7fB03B:194-227
1dTPR_1-2q7fB04B:194-227
1eTPR_1-2q7fB05B:194-227
1fTPR_1-2q7fB06B:194-227
(-)
Family: TPR_11 (16)
(-)
Family: TPR_2 (8)
(-)
Family: TPR_6 (3)
(-)
Bacillus subtilis (1)
4aTPR_6-2q7fB11B:161-193
4bTPR_6-2q7fB12B:161-193

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2Q7F)

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  2q7f
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  YRRB_BACSU | O34452
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