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(-) Description

Title :  CONFORMATIONAL CHANGE OF PSEUDOURIDINE 55 SYNTHASE UPON ITS ASSOCIATION WITH RNA SUBSTRATE
 
Authors :  K. Phannachet, R. H. Huang
Date :  16 Apr 05  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rna Modification Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Phannachet, R. H. Huang
Conformational Change Of Pseudouridine 55 Synthase Upon Its Association With Rna Substrate
Nucleic Acids Res. V. 32 1422 2004
PubMed-ID: 14990747  |  Reference-DOI: 10.1093/NAR/GKH287
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA PSEUDOURIDINE SYNTHASE B
    ChainsA, B, C, D
    EC Number4.2.1.70
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPLM1
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTRUB
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336
    SynonymTRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:17 , HIS A:34 , HOH A:328BINDING SITE FOR RESIDUE MG A 310
2AC2SOFTWAREHIS B:17 , HIS B:34 , HOH B:316BINDING SITE FOR RESIDUE MG B 310
3AC3SOFTWAREHIS C:17 , HIS C:34BINDING SITE FOR RESIDUE MG C 310
4AC4SOFTWAREHIS D:17 , HIS D:34BINDING SITE FOR RESIDUE MG D 310

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:92 -A:184
2B:92 -B:184
3C:92 -C:184
4D:92 -D:184

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZE1)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306
 
 
 
  4A:229-306
B:229-306
C:229-306
D:229-306
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306
 
 
 
  1A:229-306
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306
 
 
 
  1-
B:229-306
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306
 
 
 
  1-
-
C:229-306
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306
 
 
 
  1-
-
-
D:229-306

(-) Exons   (0, 0)

(no "Exon" information available for 1ZE1)

(-) 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:308
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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       300        
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNT 308
               SCOP domains d1ze1a2 A:1-228 Pseudouridine synthase II TruB                                                                                                                                                                                      d1ze1a1 A:229-308 Pseudouridine synthase II TruB, C-terminal domain              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh...eeee.......eeeeeeee.hhhhhhhhhhh..eeeeeeeee..ee........eee......hhhhhhhhhhhhhee................hhhhhhhh...........eeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.....hhhhhhhhhhhh..ee.hhh.....eeee...hhhhhhh...ee...eee........eeeeee....eeeeeee.....hhhhhh......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:229-306 UniProt: 229-306                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ze1 A   1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERQRRVLTLRKVFQT 308
                                    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       300        

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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       300        
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNT 308
               SCOP domains d1ze1b2 B:1-228 Pseudouridine synthase II TruB                                                                                                                                                                                      d1ze1b1 B:229-308 Pseudouridine synthase II TruB, C-terminal domain              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh...eeee.......eeeeeeee.hhhhhhhhhhh..eeeeeeeee..ee........eeee.....hhhhhhhhhhhhhee.............hhhhhhhhhhh...........eeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.....hhhhhhhhhhhh..ee.hhh.....eeee...hhhhhhh...ee...eee........eeeeee....eeeeeee.....hhhhhhhh....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: B:229-306 UniProt: 229-306                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ze1 B   1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERQRRVLTLRKVFQT 308
                                    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       300        

Chain C from PDB  Type:PROTEIN  Length:308
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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       300        
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNT 308
               SCOP domains d1ze1c2 C:1-228 Pseudouridine synthase II TruB                                                                                                                                                                                      d1ze1c1 C:229-308 Pseudouridine synthase II TruB, C-terminal domain              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh...eeee.......eeeeeeee.hhhhhhhhhhh..eeeeeeee...ee........eee......hhhhhhhhhhhhhee..............hhhhhhhh.............eeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh....eeeeeeeeee..ee.hhh.hhhhhhhhhhhh.............eeee...hhhhhhh...ee...eee........eeeeee....eeeeeee...hhhhh.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: C:229-306 UniProt: 229-306                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ze1 C   1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERQRRVLTLRKVFQT 308
                                    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       300        

Chain D from PDB  Type:PROTEIN  Length:284
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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       300        
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNT 308
               SCOP domains d1ze1d2 D:1-228 Pseudouridine synthase II TruB                                                                                                                                                                                      d1ze1d1 D:229-308 Pseudouridine synthase II TruB, C-terminal domain              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------TruB_N-1ze1D05 D:24-171                                                                                                                             ----------------------------------------------------------PUA-1ze1D01 D:230-300                                                  -------- Pfam domains (1)
           Pfam domains (2) -----------------------TruB_N-1ze1D06 D:24-171                                                                                                                             ----------------------------------------------------------PUA-1ze1D02 D:230-300                                                  -------- Pfam domains (2)
           Pfam domains (3) -----------------------TruB_N-1ze1D07 D:24-171                                                                                                                             ----------------------------------------------------------PUA-1ze1D03 D:230-300                                                  -------- Pfam domains (3)
           Pfam domains (4) -----------------------TruB_N-1ze1D08 D:24-171                                                                                                                             ----------------------------------------------------------PUA-1ze1D04 D:230-300                                                  -------- Pfam domains (4)
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh...eeee.......eeeeeeee.hhhhhhhhhhhh.eeeeeeeee..ee........eee......hhhhhhhhhhhhh.........------------------------.....eeeeeeee....eeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee..ee..........hhhhhhh..ee.hhh.....eeee...hhhhhhh...ee...eee........eeeee.....eeeeeee....hhhhhhh......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: D:229-306 UniProt: 229-306                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ze1 D   1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPA------------------------PKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERQRRVLTLRKVFQT 308
                                    10        20        30        40        50        60        70        80        90       100       110     |   -         -         -|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                                                             116                      141                                                                                                                                                                       

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZE1)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: PUA (42)
(-)
Family: PUA (12)
1aPUA-1ze1D01D:230-300
1bPUA-1ze1D02D:230-300
1cPUA-1ze1D03D:230-300
1dPUA-1ze1D04D:230-300
(-)
Family: TruB_N (12)
2aTruB_N-1ze1D05D:24-171
2bTruB_N-1ze1D06D:24-171
2cTruB_N-1ze1D07D:24-171
2dTruB_N-1ze1D08D:24-171

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TRUB_THEMA | Q9WZW0)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRUB_THEMA | Q9WZW01r3e 1ze2 2ab4

(-) Related Entries Specified in the PDB File

1ze2 THE SAME PROTEIN COMPLEXED WITH RNA