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(-) Description

Title :  CRYSTAL STRUCTURE OF TT1020 FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Wang, H. Sakai, C. Takemoto-Hori, T. Kaminishi, T. Terada, S. Kurami M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Nov 03  (Deposition) - 23 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Signal Transducing Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakai, H. Wang, C. Takemoto-Hori, T. Kaminishi, H. Yamaguchi, Y. Kamewari, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structures Of The Signal Transducing Protein Glnk From Thermus Thermophilus Hb8.
J. Struct. Biol. V. 149 99 2005
PubMed-ID: 15629661  |  Reference-DOI: 10.1016/J.JSB.2004.08.007

(-) Compounds

Molecule 1 - NITROGEN REGULATORY PROTEIN P-II
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:7 , GLY A:35 , HIS A:36 , GLY A:37 , GLY A:38 , GLU A:39 , VAL A:86 , GLY A:87 , ASP A:88 , GLY A:89 , LYS A:90 , HOH A:201 , HOH A:202 , GLY B:27 , LEU B:28 , THR B:29 , GLU B:62 , GLY B:64 , ARG B:101 , ARG B:103BINDING SITE FOR RESIDUE ATP A 200
2AC2SOFTWAREILE B:7 , GLY B:35 , HIS B:36 , GLY B:37 , LYS B:58 , VAL B:86 , GLY B:87 , ASP B:88 , GLY B:89 , LYS B:90 , HOH B:303 , HOH B:316 , HOH B:337 , GLY C:27 , LEU C:28 , THR C:29 , GLU C:62 , GLY C:64 , ARG C:101 , ARG C:103BINDING SITE FOR RESIDUE ATP B 300
3AC3SOFTWAREGLY A:27 , LEU A:28 , THR A:29 , GLU A:62 , GLY A:64 , ARG A:101 , ARG A:103 , ILE C:7 , GLY C:35 , HIS C:36 , GLY C:37 , LYS C:58 , VAL C:86 , GLY C:87 , ASP C:88 , GLY C:89 , LYS C:90 , HOH C:418 , HOH C:429BINDING SITE FOR RESIDUE ATP C 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V3S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V3S)

(-) Exons   (0, 0)

(no "Exon" information available for 1V3S)

(-) 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:97
 aligned with P83820_THETH | P83820 from UniProtKB/TrEMBL  Length:116

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         P83820_THETH     1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEEDEA 110
               SCOP domains d1v3sa_ A: PII (product of glnB)                                                                               SCOP domains
               CATH domains 1v3sA00 A:1-110  [code=3.30.70.120, no n             ame defined]                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee....-------------..eeeeeeeeeehhhhhhhhhhhhhhhh........eeeeee..eeee.....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1v3s A   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHGGET-------------ELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEEDEA 110
                                    10        20        30        40         -   |    60        70        80        90       100       110
                                                                  40            54                                                        


Chain A from PDB  Type:PROTEIN  Length:97
 aligned with Q5SM86_THET8 | Q5SM86 from UniProtKB/TrEMBL  Length:116

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         Q5SM86_THET8     1 MKLIVAIVRPEKLNEVLEALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEEDEA 110
               SCOP domains d1v3sa_ A: PII (product of glnB)                                                                               SCOP domains
               CATH domains 1v3sA00 A:1-110  [code=3.30.70.120, no n             ame defined]                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee....-------------..eeeeeeeeeehhhhhhhhhhhhhhhh........eeeeee..eeee.....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1v3s A   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHGGET-------------ELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEEDEA 110
                                    10        20        30        40         -   |    60        70        80        90       100       110
                                                                  40            54                                                        


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with P83820_THETH | P83820 from UniProtKB/TrEMBL  Length:116

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
         P83820_THETH     1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
               SCOP domains d1v3sb_ B: PII (product of glnB)                                                                             SCOP domains
               CATH domains 1v3sB00 B:1-108  [code=3.30.70.120, n               o name defined]                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.---------------...eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1v3s B   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHG---------------MELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
                                    10        20        30      |  -         -  |     60        70        80        90       100        
                                                               37              53                                                       


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with Q5SM86_THET8 | Q5SM86 from UniProtKB/TrEMBL  Length:116

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
         Q5SM86_THET8     1 MKLIVAIVRPEKLNEVLEALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
               SCOP domains d1v3sb_ B: PII (product of glnB)                                                                             SCOP domains
               CATH domains 1v3sB00 B:1-108  [code=3.30.70.120, n               o name defined]                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.---------------...eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1v3s B   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHG---------------MELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
                                    10        20        30      |  -         -  |     60        70        80        90       100        
                                                               37              53                                                       


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with P83820_THETH | P83820 from UniProtKB/TrEMBL  Length:116

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
         P83820_THETH     1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
               SCOP domains d1v3sc_ C: PII (product of glnB)                                                                             SCOP domains
               CATH domains 1v3sC00 C:1-108  [code=3.30.70.120, n                 o name defined]                                        CATH domains
           Pfam domains (1) ---P-II-1v3sC01 C:4-105                                                                                  --- Pfam domains (1)
           Pfam domains (2) ---P-II-1v3sC02 C:4-105                                                                                  --- Pfam domains (2)
           Pfam domains (3) ---P-II-1v3sC03 C:4-105                                                                                  --- Pfam domains (3)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.-----------------.eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1v3s C   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHG-----------------LHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
                                    10        20        30      |  -         -    |   60        70        80        90       100        
                                                               37                55                                                     


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with Q5SM86_THET8 | Q5SM86 from UniProtKB/TrEMBL  Length:116

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
         Q5SM86_THET8     1 MKLIVAIVRPEKLNEVLEALFQAEVRGLTLSRVQGHGGETERVETYRGTTVKMELHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
               SCOP domains d1v3sc_ C: PII (product of glnB)                                                                             SCOP domains
               CATH domains 1v3sC00 C:1-108  [code=3.30.70.120, n                 o name defined]                                        CATH domains
           Pfam domains (1) ---P-II-1v3sC01 C:4-105                                                                                  --- Pfam domains (1)
           Pfam domains (2) ---P-II-1v3sC02 C:4-105                                                                                  --- Pfam domains (2)
           Pfam domains (3) ---P-II-1v3sC03 C:4-105                                                                                  --- Pfam domains (3)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.-----------------.eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1v3s C   1 MKLIVAIVRPEKLNEVLKALFQAEVRGLTLSRVQGHG-----------------LHEKVRLEIGVSEPFVKPTVEAILKAARTGEVGDGKIFVLPVEKVYRIRTGEED 108
                                    10        20        30      |  -         -    |   60        70        80        90       100        
                                                               37                55
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: GlnB-like (50)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q5SM86_THET8 | Q5SM86)
molecular function
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
biological process
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    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.

Chain A,B,C   (P83820_THETH | P83820)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    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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  1v3s
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q5SM86_THET8 | Q5SM86: 1v3r
UniProtKB/TrEMBL
        P83820_THETH | P83820: 1ufl 1v3r 1v9o 1vfj

(-) Related Entries Specified in the PDB File

1v3r THE SAME PROTEIN RELATED ID: TTK003001020.3 RELATED DB: TARGETDB