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(-) Description

Title :  CRYSTAL STRUCTURE OF TT0907 FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Idaka, H. Yagi, K. Murayama, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 May 04  (Deposition) - 17 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Idaka, H. Yagi, K. Murayama, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of Tt0907 From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TT0907
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:61 , THR A:184 , ALA A:185 , GLY A:257 , THR A:258 , THR A:259 , THR A:299 , ASN A:300 , HIS A:302 , LEU A:308 , HOH A:1325 , HOH A:1335 , HOH A:1479 , HOH A:1495BINDING SITE FOR RESIDUE CIT A 1322

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:22 -Pro A:23
2Pro A:287 -Pro A:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WDI)

(-) Sequences/Alignments

Asymmetric/Biological 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:294
 aligned with QUEA_THET2 | Q72JS5 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    
           QUEA_THET2     2 EGLEAYDYHLPPEQIAQEGVEPRDMARLMVVYREGPFRVAHKRVRDLPEFLRPGDVLVFNESKVIPARLLARKPTGGKVEILLVRERSPGLWEALLGPARKAPPGTRLLLLSPKDLAPVPGLQAEVVAVEEDGVRLLRFQGDLVAHLEEVGEVPLPPYIKAKIPMERYQTVYARRPGSVAAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRPVKGDPEKHEMHAEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLFIRPPYTFKVVDALFTNFHLPRSTLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLIL 345
               SCOP domains d1wdia_ A: Queuosine biosynthesis protein queA                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Queuosine_synth-1wdiA01 A:3-345                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author hhhhhhh...hhhhh......hhhh.eeeeee......eeeee..hhhhhh....eeeeeeeee..eeeeee.....eeeeee....------............eeeee.......eeeeeeee.......----------..eee.......-------------------------...hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh..---------...eeeeehhhhhhhhhhhhhh...eeeehhhhhhhhhhhee...ee..eeeee..............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wdi A   2 EGLEAYDYHLPPEQIAQEGVEPRDMARLMVVYREGPFRVAHKRVRDLPEFLRPGDVLVFNESKVIPARLLARKPTGGKVEILLVRER------ALLGPARKAPPGTRLLLLSPKDLAPVPGLQAEVVAVEED----------LVAHLEEVGEVP-------------------------AAPTAGLHFTPELLERLREMGVELRFLTLHVGPGTFRP---------MHAEPYAIPEEVAEAVNRAKAEGRRVVAVGTTVVRALESAYREGVGVVAGEGETRLFIRPPYTFKVVDALFTNFHLPRSTLLMLVAAFLGRERTLEAYRLAVAEGYRFYSLGDAMLIL 345
                                    11        21        31        41        51        61        71        81      |  -   |   101       111       121       131 |       -  |    151   |     -         -       181       191       201       211      |  -      |231       241       251       261       271       281       291       301       311       321       331       341    
                                                                                                                 88     95                                   133        144        155                       181                                  218       228
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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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Queuosine_synth] (3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (QUEA_THET2 | Q72JS5)
molecular function
    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: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.
biological process
    GO:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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