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(-) Description

Title :  CRYSTAL STRUCTURE OF HUTP, AN RNA BINDING ANTITERMINATION PROTEIN
 
Authors :  T. S. Kumarevel, Z. Fujimoto, P. Karthe, M. Oda, H. Mizuno, P. K. R. Kumar
Date :  29 Mar 04  (Deposition) - 20 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hutp, Antiterminator, Rna Binding Protein, Regulation Of Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, Z. Fujimoto, P. Karthe, M. Oda, H. Mizuno, P. K. R. Kuma
Crystal Structure Of Activated Hutp; An Rna Binding Protein That Regulates Transcription Of The Hut Operon In Bacillus Subtilis
Structure V. 12 1269 2004
PubMed-ID: 15242603  |  Reference-DOI: 10.1016/J.STR.2004.05.005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUT OPERON POSITIVE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET5A, PETHP4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RNA-BINDING, ANTITERMINATOR PROTEIN
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: HUTP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HBN1Ligand/IonN-(2-NAPHTHYL)HISTIDINAMIDE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1HBN3Ligand/IonN-(2-NAPHTHYL)HISTIDINAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:85 , ARG A:88 , GLU A:139 , THR A:140 , PHE A:141 , GLU B:81 , HIS B:84 , GLY B:85 , VAL B:143 , HOH B:1003BINDING SITE FOR RESIDUE HBN B 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VEA)

(-) 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:143
 aligned with HUTP_BACSU | P10943 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   
           HUTP_BACSU     6 ERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
               SCOP domains d1veaa_ A: Hut operon positive regulatory protein HutP                                                                                          SCOP domains
               CATH domains 1veaA00 A:6-148 Hut operon positive regulatory protein HutP                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eeeeeeeeee..........eeeeeeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vea A   6 ERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with HUTP_BACSU | P10943 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
           HUTP_BACSU     5 KERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
               SCOP domains d1veab_ B: Hut operon positive regulatory protein HutP                                                                                           SCOP domains
               CATH domains 1veaB00 B:5-148 Hut operon positive regulatory protein HutP                                                                                      CATH domains
           Pfam domains (1) ---HutP-1veaB01 B:8-146                                                                                                                       -- Pfam domains (1)
           Pfam domains (2) ---HutP-1veaB02 B:8-146                                                                                                                       -- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh.....eeeeeeeeee..........eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vea B   5 KERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: HutP] (9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HUTP_BACSU | P10943)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
    GO:0006547    histidine metabolic process    The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  HUTP_BACSU | P10943
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 Related Entries

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

UniProtKB/Swiss-Prot
        HUTP_BACSU | P10943: 1wmq 1wps 1wpt 1wpu 1wpv 1wrn 1wro 1wrq 3boy 4h4l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VEA)