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(-) Description

Title :  CRYSTAL STRUCTURE OF APE0204 FROM AEROPYRUM PERNIX
 
Authors :  M. Kato-Murayama, Y. Bessho, M. Shirouzu, S. Yokoyama, Riken Structu Genomics/Proteomics Initiative (Rsgi)
Date :  27 May 04  (Deposition) - 27 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Rna 2'-Phosphotransferase, Trna Splicing, Nad, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kato-Murayama, Y. Bessho, M. Shirouzu, S. Yokoyama
Crystal Structure Of The Rna 2'-Phosphotransferase From Aeropyrum Pernix K1
J. Mol. Biol. V. 348 295 2005
PubMed-ID: 15811369  |  Reference-DOI: 10.1016/J.JMB.2005.02.049

(-) Compounds

Molecule 1 - PROBABLE RNA 2'-PHOSPHOTRANSFERASE
    Chains: A
    EC Number: 2.7.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-186
    Gene: APE0204
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: RNA 2'-PHOSPHOTRANSFERASE, APE0204 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:58 , HOH A:316BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREARG A:14 , LYS A:61 , ARG A:63BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWAREARG A:150BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWAREHIS A:15 , ARG A:115BINDING SITE FOR RESIDUE CL A 204
5AC5SOFTWAREARG A:158BINDING SITE FOR RESIDUE CL A 206

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:148 -A:173

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WFX)

(-) 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:180
 aligned with KPTA_AERPE | Q9YFP5 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:180
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
           KPTA_AERPE    37 VRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIPVNVEPLPGEPPPILYHGTTEEALPLIMERGIMRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERMSKTVYTVDWVPPECIAEVRRESL 216
               SCOP domains d1wfxa_ A: Probable RNA 2'-phosphotransferase KptA                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains PTS_2-RNA-1wfxA01 A:3-169                                                                                                                                              ------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhh........eehhhhhhhhhhh.....hhhhhhhhhhhh....eeee..eeee...................eeee..hhhhhhhhhhhh........eeee.hhhhhhhhhh......eeeeeehhhhhhh....ee....eeee...hhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wfx A   3 VRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIPVNVEPLPGEPPPILYHGTTEEALPLImERGImRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERmSKTVYTVDWVPPECIAEVRRESL 182
                                    12        22        32        42        52        62        72        82        92       102    |  112       122       132       142       152      |162       172       182
                                                                                                                                  107-MSE|                                            159-MSE                   
                                                                                                                                       112-MSE
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  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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: PTS_2-RNA] (1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (KPTA_AERPE | Q9YFP5)
molecular function
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

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