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(-) Description

Title :  CRYSTAL STRUCTURE OF PH1313 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  M. Sugahara, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Feb 04  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrococcus Horikoshii, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, S. Murai, M. Sugahara, N. Kunishima
Purification, Crystallization And Preliminary Crystallographic Analysis Of The Putative Thiamine-Biosynthesis Protein Ph1313 From Pyrococcus Horikoshii Ot3
Acta Crystallogr. , Sect. F V. 63 56 2007
PubMed-ID: 17183176  |  Reference-DOI: 10.1107/S1744309106054509

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1313
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:111 , GLN A:128 , HOH A:1068BINDING SITE FOR RESIDUE MRD A 1001
2AC2SOFTWAREALA A:192 , LEU A:193 , LEU A:305 , LEU A:307 , HOH A:1283BINDING SITE FOR RESIDUE MRD A 1002
3AC3SOFTWAREHOH A:1128 , ARG B:110 , VAL B:111 , GLN B:128 , GLY B:132BINDING SITE FOR RESIDUE MRD B 1003
4AC4SOFTWAREALA B:192 , LEU B:223 , LEU B:305 , LEU B:307 , HOH B:1115 , HOH B:1235BINDING SITE FOR RESIDUE MRD B 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VBK)

(-) 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:307
 aligned with O59053_PYRHO | O59053 from UniProtKB/TrEMBL  Length:307

    Alignment length:307
                                    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       
         O59053_PYRHO     1 MNVVIVRYGEIGTKSRQTRSWFEKILMNNIREALVTEEVPYKEIFSRHGRIIVKTNSPKEAANVLVRVFGIVSISPAMEVEASLEKINRTALLMFRKKAKEVGKERPKFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEKIKGWGGLPIGTEGRMIGILHDELSALAIFLMMKRGVEVIPVYIGKDDKNLEKVRSLWNLLKRYSYGSKGFLVVAESFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYPLIALPEEYIKSVKERLGL 307
               SCOP domains d1vbka2 A:1-175 Hypothetical protein PH1313, N-terminal domain                                                                                                                 d1vbka1 A:176-307 Hypothetical protein PH1313, C-terminal domain                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeee..hhhhhhhhhh....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh..ee......eeeeeeee..eeeee...ee...........eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhh..eee...hhhhh...hhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbk A   1 MNVVIVRYGEIGTKSRQTRSWFEKILMNNIREALVTEEVPYKEIFSRHGRIIVKTNSPKEAANVLVRVFGIVSISPAMEVEASLEKINRTALLMFRKKAKEVGKERPKFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEKIKGWGGLPIGTEGRMIGILHDELSALAIFLMMKRGVEVIPVYIGKDDKNLEKVRSLWNLLKRYSYGSKGFLVVAESFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYPLIALPEEYIKSVKERLGL 307
                                    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:296
 aligned with O59053_PYRHO | O59053 from UniProtKB/TrEMBL  Length:307

    Alignment length:307
                                    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       
         O59053_PYRHO     1 MNVVIVRYGEIGTKSRQTRSWFEKILMNNIREALVTEEVPYKEIFSRHGRIIVKTNSPKEAANVLVRVFGIVSISPAMEVEASLEKINRTALLMFRKKAKEVGKERPKFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEKIKGWGGLPIGTEGRMIGILHDELSALAIFLMMKRGVEVIPVYIGKDDKNLEKVRSLWNLLKRYSYGSKGFLVVAESFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYPLIALPEEYIKSVKERLGL 307
               SCOP domains d1vbkb2      B:1-175 Hypothetical protein PH1313, N-terminal domain                                                                                                            d1vbkb1 B:176-307 Hypothetical protein PH1313, C-terminal domain                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------THUMP-1vbkB03 B:72-167                                                                          ---------ThiI-1vbkB01 B:177-259                                                             ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------THUMP-1vbkB04 B:72-167                                                                          ---------ThiI-1vbkB02 B:177-259                                                             ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeee.-----....hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeee..hhhhhhhhhh....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhh....ee......eeeeeeee..eeeee...eeeee........eeeee..hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhh....ee.....------hhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbk B   1 MNVVIVRY-----KSRQTRSWFEKILMNNIREALVTEEVPYKEIFSRHGRIIVKTNSPKEAANVLVRVFGIVSISPAMEVEASLEKINRTALLMFRKKAKEVGKERPKFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEKIKGWGGLPIGTEGRMIGILHDELSALAIFLMMKRGVEVIPVYIGKDDKNLEKVRSLWNLLKRYSYGSKGFLVVAESFDRVLKLIRDFGVKGVIKGLRP------VSEITEDFKMFPVPVYYPLIALPEEYIKSVKERLGL 307
                                   | -   |    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    |    - |     280       290       300       
                                   8    14                                                                                                                                                                                                                                                        265    272
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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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: THUMP] (1)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O59053_PYRHO | O59053)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004810    tRNA adenylyltransferase activity    Catalysis of the reaction: ATP + tRNA(n) = diphosphate + tRNA(n+1).

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