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(-) Description

Title :  STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)
 
Authors :  B. N. Chaudhuri, S. Chan, L. J. Perry, T. O. Yeates, Tb Structural Geno Consortium (Tbsgc)
Date :  24 Feb 04  (Deposition) - 02 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hinged Motion, Trna Modification, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. N. Chaudhuri, S. Chan, L. J. Perry, T. O. Yeates
Crystal Structure Of The Apo Forms Of Psi 55 Trna Pseudouridine Synthase From Mycobacterium Tuberculosis: A Hinge At The Base Of The Catalytic Cleft.
J. Biol. Chem. V. 279 24585 2004
PubMed-ID: 15028724  |  Reference-DOI: 10.1074/JBC.M401045200

(-) Compounds

Molecule 1 - TRNA PSEUDOURIDINE SYNTHASE B
    Chains: A, B
    EC Number: 4.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)-GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRUB, RV2793C, MT2862.1, MTV002.58C, MB2816C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE

 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 1SGV)

(-) Sites  (0, 0)

(no "Site" information available for 1SGV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SGV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SGV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SGV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SGV)

(-) Exons   (0, 0)

(no "Exon" information available for 1SGV)

(-) 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:262
 aligned with TRUB_MYCTO | P9WHP6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:290
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
           TRUB_MYCTO     3 ATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRP 292
               SCOP domains d1sgva2 A:3-235 Pseudouridine synthase II TruB                                                                                                                                                                                           d1sgva1 A:236-292                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhh....eeeeeeeee.eee........eeee......hhhhhhhhhhhh.eee----------------------------.....eeeeeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh.hhhhhhhh....eehhhhhhhhheeee.hhhhhhhhhh............eeee.....eeeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgv A   3 ATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEI----------------------------LEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRP 292
                                    12        22        32        42        52        62        72        82        92       102       112 |       -         -         -|      152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
                                                                                                                                         114                          143                                                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:262
 aligned with TRUB_MYCTU | P9WHP7 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:290
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
           TRUB_MYCTU     3 ATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRP 292
               SCOP domains d1sgva2 A:3-235 Pseudouridine synthase II TruB                                                                                                                                                                                           d1sgva1 A:236-292                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhh....eeeeeeeee.eee........eeee......hhhhhhhhhhhh.eee----------------------------.....eeeeeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh.hhhhhhhh....eehhhhhhhhheeee.hhhhhhhhhh............eeee.....eeeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgv A   3 ATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEI----------------------------LEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRP 292
                                    12        22        32        42        52        62        72        82        92       102       112 |       -         -         -|      152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
                                                                                                                                         114                          143                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with TRUB_MYCTO | P9WHP6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
           TRUB_MYCTO     1 MSATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPAT 294
               SCOP domains d1sgvb2 B:1-235 Pseudouridine synthase II TruB                                                                                                                                                                                             d1sgvb1 B:236-294                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------TruB_N-1sgvB03 B:27-179                                                                                                                                  --------------------------------------------------------TruB_C-1sgvB01 B:236-291                                --- Pfam domains (1)
           Pfam domains (2) --------------------------TruB_N-1sgvB04 B:27-179                                                                                                                                  --------------------------------------------------------TruB_C-1sgvB02 B:236-291                                --- Pfam domains (2)
         Sec.struct. author ......eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee.eee........eeee......hhhhhhhhhhhhh----------------------------..........eeeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh.hhhhhhhh....eehhhhhhhhheeee.hhhhhhhhhh............eeee.....eeeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sgv B   1 MSATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLR----------------------------SVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPAT 294
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
                                                                                                                                        111                          140                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with TRUB_MYCTU | P9WHP7 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
           TRUB_MYCTU     1 MSATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPAT 294
               SCOP domains d1sgvb2 B:1-235 Pseudouridine synthase II TruB                                                                                                                                                                                             d1sgvb1 B:236-294                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------TruB_N-1sgvB03 B:27-179                                                                                                                                  --------------------------------------------------------TruB_C-1sgvB01 B:236-291                                --- Pfam domains (1)
           Pfam domains (2) --------------------------TruB_N-1sgvB04 B:27-179                                                                                                                                  --------------------------------------------------------TruB_C-1sgvB02 B:236-291                                --- Pfam domains (2)
         Sec.struct. author ......eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee.eee........eeee......hhhhhhhhhhhhh----------------------------..........eeeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh.hhhhhhhh....eehhhhhhhhheeee.hhhhhhhhhh............eeee.....eeeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sgv B   1 MSATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLR----------------------------SVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPAT 294
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
                                                                                                                                        111                          140
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SGV)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: PUA (42)
(-)
Clan: no clan defined [family: TruB_N] (12)

(-) Gene Ontology  (11, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRUB_MYCTO | P9WHP6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0031119    tRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Chain A,B   (TRUB_MYCTU | P9WHP7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:1990481    mRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0031119    tRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

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