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(-) Description

Title :  CRYSTAL STRUCTURE OF PH0300
 
Authors :  H. Nakagawa, M. Kuratani, S. Goto-Ito, T. Ito, S. I. Sekine, S. Yokoyama
Date :  10 Apr 12  (Deposition) - 13 Mar 13  (Release) - 13 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Atpase, Trna Modification Enzyme, Thiolation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nakagawa, M. Kuratani, S. Goto-Ito, T. Ito, K. Katsura, T. Terada, M. Shirouzu, S. I. Sekine, N. Shigi, S. Yokoyama
Crystallographic And Mutational Studies On The Trna Thiouridine Synthetase Ttua.
Proteins 2013
PubMed-ID: 23444054  |  Reference-DOI: 10.1002/PROT.24273

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH0300
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PH0300
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT-3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BCN1Ligand/IonBICINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BCN2Ligand/IonBICINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:3 , CYS A:6 , CYS A:22 , HIS A:25BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS A:272 , CYS A:275 , CYS A:284 , CYS A:287BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREALA A:53 , SER A:55 , GLY A:57 , ASP A:59 , SER A:60 , THR A:153 , GLY A:154 , ASP A:159BINDING SITE FOR RESIDUE BCN A 403

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:128 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:16 -Pro A:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VRH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VRH)

(-) Exons   (0, 0)

(no "Exon" information available for 3VRH)

(-) 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:298
 aligned with O58038_PYRHO | O58038 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                    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         
         O58038_PYRHO     1 MKCKFCSREAYIKIHYPKMYLCEEHFKEYFERKVSRTIERYKLLTKDERILVAVSGGKDSAVTAYVLKKLGYNIECLHINLGISGYSEKSEEYAKKQCKLIGAPLHIVRIKEILGYGIGEVKTRRPPCSYCGLTKRYIMNKFAYDNGFDAIATGHNLDDEASFLLNNILHWNTEYLAKGGPILPQQGKFIKKVKPLYEVTEREVVAYALAVGLEYIVEECPYARGATTLDMKGVLNELEEKRPGTKFNFVRGYLKKKKLFEPEIKEKEIKECKICRMPSSGDICAFCKFWGLKKEINFKVSSTDEEPFG 309
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeehhhhhh..........hhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhh.hhhhhhh...ee.......eee......hhhhhhhhhhhhh..........----.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.-------..............hhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrh A   1 MKCKFCSREAYIKIHYPKMYLCEEHFKEYFERKVSRTIERYKLLTKDERILVAVSGGKDSAVTAYVLKKLGYNIECLHINLGISGYSEKSEEYAKKQCKLIGAPLHIVRIKEILGYGIGEVKTRRPPCSYCGLTKRYIMNKFAYDNGFDAIATGHNLDDEASFLLNNILHWNTEYLAKGGPILPQQGKFIKKVKPLYEVTEREVVAYALAVGLEYIVEECPY----TTLDMKGVLNELEEKRPGTKFNFVRGYLKKKKLFEP-------KECKICRMPSSGDICAFCKFWGLKKEINFKVSSTDEEPFG 309
                                    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         
                                                                                                                                                                                                                                                       222  227                                262     270
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3VRH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VRH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VRH)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (O58038_PYRHO | O58038)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    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:0034227    tRNA thio-modification    The addition a sulfur atom to a nucleotide in a tRNA molecule.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.

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  3vrh
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 Related Entries

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

UniProtKB/Swiss-Prot
        O58038_PYRHO | O58038: 5mko 5mkp 5mkq

(-) Related Entries Specified in the PDB File

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