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(-) Description

Title :  CRYSTAL STRUCTURES OF TRYPANOSOMA BRUCIEI MRP1/MRP2
 
Authors :  M. A. Schumacher, E. Karamooz, A. Zikova, L. Trantirek, J. Lukes
Date :  28 Mar 06  (Deposition) - 05 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B,D,G,H,J,K,P
Biol. Unit 1:  A,B,D,G  (1x)
Biol. Unit 2:  H,J,K,P  (1x)
Keywords :  T. Brucei; Guide Rna; Matchmaking; Rna Editing, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, E. Karamooz, A. Zikova, L. Trantirek, J. Lukes
Crystal Structures Of T. Brucei Mrp1/Mrp2 Guide-Rna Binding Complex Reveal Rna Matchmaking Mechanism.
Cell(Cambridge, Mass. ) V. 126 701 2006
PubMed-ID: 16923390  |  Reference-DOI: 10.1016/J.CELL.2006.06.047

(-) Compounds

Molecule 1 - MITOCHONDRIAL RNA-BINDING PROTEIN 2
    Chains: A, G, H, P
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID, COEXPRESSION
    Gene: MRP1
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 185431
    Strain: TREU927
    Synonym: MRP2, GUIDE RNA-BINDING PROTEIN
 
Molecule 2 - MITOCHONDRIAL RNA-BINDING PROTEIN 1
    Chains: B, D, K, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID, COEXPRESSION
    Gene: MRP2
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 185431
    Strain: TREU927
    Synonym: MRP1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABDGHJKP
Biological Unit 1 (1x): ABDG    
Biological Unit 2 (1x):     HJKP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2GID)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GID)

(-) Exons   (0, 0)

(no "Exon" information available for 2GID)

(-) 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:150
 aligned with Q952G2_9TRYP | Q952G2 from UniProtKB/TrEMBL  Length:224

    Alignment length:162
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
         Q952G2_9TRYP    60 SLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARMLTEEGNKAERVVSVMLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRPAQQKQQVAGEEGDETFEWTVEFDVAESLMLQRFLTQALHYNTGFAR 221
               SCOP domains d2gida1 A:60-221 Guide RNA binding protein gBP25                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee.........eeeeeeee..eeeeeeee.............eeeeeee..hhhhhhhhhhhh.....eee...eeeeeee.......eeeeeee...------------....eeeeeehhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gid A  60 SLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARmLTEEGNKAERVVSVmLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRP------------DETFEWTVEFDVAESLmLQRFLTQALHYNTGFAR 221
                                    69        79        89        99       109|      119     | 129       139       149       159       169     |   -       189       199    |  209       219  
                                                                            110-MSE        125-MSE                                           175          188             204-MSE             


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with P90629_9TRYP | P90629 from UniProtKB/TrEMBL  Length:206

    Alignment length:146
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167      
         P90629_9TRYP    28 SLPKFEIHDVRDDPALGTMTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRMETKAYTLDFEKSAQGYHLHGKVHRVASQRMEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
               SCOP domains d2gidb1 B:28-173 GBP21                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee...hhhh.ee..eeee..eeeeeeee................hhhhheeee.hhhhhhhhhhhhh....eeeee...eeeeeee...eeeeeeee........eeeeeeeehhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid B  28 SLPKFEIHDVRDDPAEGTmTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRmETKAYTLDFEKSAQGYHLHGKVHRVASQRmEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
                                    37        47        57        67        77        87        97       107 |     117       127       137 |     147       157       167      
                                             46-MSE                                                        109-MSE                       139-MSE                              


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with P90629_9TRYP | P90629 from UniProtKB/TrEMBL  Length:206

    Alignment length:146
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167      
         P90629_9TRYP    28 SLPKFEIHDVRDDPALGTMTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRMETKAYTLDFEKSAQGYHLHGKVHRVASQRMEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
               SCOP domains d2gidd1 D:28-173 GBP21                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhh.eeeeeeee..eeeeeeee.....................eeeeehhhhhhhhhhhhh....eeeeee..eeeeeee....eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid D  28 SLPKFEIHDVRDDPAEGTmTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRmETKAYTLDFEKSAQGYHLHGKVHRVASQRmEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
                                    37        47        57        67        77        87        97       107 |     117       127       137 |     147       157       167      
                                             46-MSE                                                        109-MSE                       139-MSE                              


Chain G from PDB  Type:PROTEIN  Length:151
 aligned with Q952G2_9TRYP | Q952G2 from UniProtKB/TrEMBL  Length:224

    Alignment length:163
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
         Q952G2_9TRYP    59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARMLTEEGNKAERVVSVMLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRPAQQKQQVAGEEGDETFEWTVEFDVAESLMLQRFLTQALHYNTGFAR 221
               SCOP domains d2gidg1 G:59-221 Guide RNA binding protein gBP25                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee.........eeeeeeee..eeeeeeeee..........eeeeeeeeeehhhhhhhhhhhhh....eeee....eeeeee.......eeeeeeee..------------..eeeeeeeehhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid G  59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARmLTEEGNKAERVVSVmLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRP------------DETFEWTVEFDVAESLmLQRFLTQALHYNTGFAR 221
                                    68        78        88        98       108 |     118      |128       138       148       158       168      |  -       188       198     | 208       218   
                                                                             110-MSE        125-MSE                                           175          188             204-MSE             


Chain H from PDB  Type:PROTEIN  Length:151
 aligned with Q952G2_9TRYP | Q952G2 from UniProtKB/TrEMBL  Length:224

    Alignment length:163
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
         Q952G2_9TRYP    59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARMLTEEGNKAERVVSVMLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRPAQQKQQVAGEEGDETFEWTVEFDVAESLMLQRFLTQALHYNTGFAR 221
               SCOP domains d2gidh1 H:59-221 Guide RNA binding protein gBP25                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.....eee.......hhhhh...eeeee..eee..eeee..........eeeee....hhhhhhhhhhhhhh....eee.....eeeeee.......eeeeeeee..------------..eeeeee..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid H  59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARmLTEEGNKAERVVSVmLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRP------------DETFEWTVEFDVAESLmLQRFLTQALHYNTGFAR 221
                                    68        78        88        98       108 |     118      |128       138       148       158       168      |  -       188       198     | 208       218   
                                                                             110-MSE        125-MSE                                           175          188             204-MSE             


Chain J from PDB  Type:PROTEIN  Length:146
 aligned with P90629_9TRYP | P90629 from UniProtKB/TrEMBL  Length:206

    Alignment length:146
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167      
         P90629_9TRYP    28 SLPKFEIHDVRDDPALGTMTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRMETKAYTLDFEKSAQGYHLHGKVHRVASQRMEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
               SCOP domains d2gidj1 J:28-173 GBP21                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeeeee..eeeeeeee.....................eeee.hhhhhhhhhhhhh....eeeee....eeeeee...eeeeeeee........eeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid J  28 SLPKFEIHDVRDDPAEGTmTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRmETKAYTLDFEKSAQGYHLHGKVHRVASQRmEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
                                    37        47        57        67        77        87        97       107 |     117       127       137 |     147       157       167      
                                             46-MSE                                                        109-MSE                       139-MSE                              


Chain K from PDB  Type:PROTEIN  Length:146
 aligned with P90629_9TRYP | P90629 from UniProtKB/TrEMBL  Length:206

    Alignment length:146
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167      
         P90629_9TRYP    28 SLPKFEIHDVRDDPALGTMTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRMETKAYTLDFEKSAQGYHLHGKVHRVASQRMEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
               SCOP domains d2gidk1 K:28-173 GBP21                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeeeee..eeeeee..................hhhhhee....hhhhhhhhhhhh....eeee....eeeeeee...eeeeeeee.........eeeeeeehhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid K  28 SLPKFEIHDVRDDPAEGTmTRVAVDGKLLLISQYPQLGPRKVDPNDLSPQFDADRRISVRLRHVDLAYLVGVCKERVPRHRmETKAYTLDFEKSAQGYHLHGKVHRVASQRmEDWSVKFDNHFAVTLEHFLESALDESFGFRQHYA 173
                                    37        47        57        67        77        87        97       107 |     117       127       137 |     147       157       167      
                                             46-MSE                                                        109-MSE                       139-MSE                              


Chain P from PDB  Type:PROTEIN  Length:151
 aligned with Q952G2_9TRYP | Q952G2 from UniProtKB/TrEMBL  Length:224

    Alignment length:163
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
         Q952G2_9TRYP    59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARMLTEEGNKAERVVSVMLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRPAQQKQQVAGEEGDETFEWTVEFDVAESLMLQRFLTQALHYNTGFAR 221
               SCOP domains d2gidp1 P:59-221 Guide RNA binding protein gBP25                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.........eeeee..hhhhh...eeeeeeee..eeeeeeeee..........ee.........hhhhhhhhhhh............eeeeeee.......eeeeeee...------------...eeeeeeehhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gid P  59 PSLAQQRARRAQLPPAFDVVHWNDEDISRGHLLRVLHRDTFVVLDYHRQARmLTEEGNKAERVVSVmLPAVYTARFLAVLEGRSEKVEVHSRYTNATFTPNPAAPYTFTLKCTSTRP------------DETFEWTVEFDVAESLmLQRFLTQALHYNTGFAR 221
                                    68        78        88        98       108 |     118      |128       138       148       158       168      |  -       188       198     | 208       218   
                                                                             110-MSE        125-MSE                                           175          188             204-MSE
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GID)

(-) Gene Ontology  (6, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,G,H,P   (Q952G2_9TRYP | Q952G2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B,D,J,K   (P90629_9TRYP | P90629)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0016556    mRNA modification    The covalent alteration of one or more nucleotides within an mRNA molecule to produce an mRNA molecule with a sequence that differs from that coded genetically.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  2gid
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  Q952G2_9TRYP | Q952G2
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 Related Entries

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

UniProtKB/TrEMBL
        P90629_9TRYP | P90629: 2gia 2gje
        Q952G2_9TRYP | Q952G2: 2gia 2gje

(-) Related Entries Specified in the PDB File

2gia 2gje