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(-) Description

Title :  CRYSTAL STRUCTURE OF NUSA FROM THERMOTOGA MARITIMA: A STRUCTURE-BASED ROLE OF THE N-TERMINAL DOMAIN
 
Authors :  D. H. Shin, H. H. Nguyen, J. Jancarik, H. Yokota, R. Kim, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  20 Feb 02  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Nusa, Crystal Structure, Ob Fold Kh Domain, Rna Polymerase, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, H. H. Nguyen, J. Jancarik, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Nusa From Thermotoga Maritima And Functional Implication Of The N-Terminal Domain.
Biochemistry V. 42 13429 2003
PubMed-ID: 14621988  |  Reference-DOI: 10.1021/BI035118H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N UTILIZATION SUBSTANCE PROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA PLYSS.RARE
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PSKB3
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: NUSA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1L2F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L2F)

(-) Exons   (0, 0)

(no "Exon" information available for 1L2F)

(-) 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:344
 aligned with Q9X298_THEMA | Q9X298 from UniProtKB/TrEMBL  Length:344

    Alignment length:344
                                    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       310       320       330       340    
         Q9X298_THEMA     1 MNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDPNVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMNL 344
               SCOP domains d1l2fa4 A:1-126 Transcription factor NusA, N-terminal domain                                                                  d1l2fa1 A:127-198 S1 domain of NusA                                     d1l2fa2 A:199-276 Transcription factor NusA, C-terminal domains               d1l2fa3 A:277-344 Transcription factor NusA, C-terminal domains      SCOP domains
               CATH domains -1l2fA01 A:2-125  [code=3.30.1480.10, no name defined]                                                                       ---------1l2fA02 A:135-197 Nucleic acid-binding proteins                1l2fA03 A:198-276  [code=3.30.300.20, no name defined]                         1l2fA04 A:277-344  [code=3.30.300.20, no name defined]               CATH domains
               Pfam domains ---NusA_N-1l2fA02 A:4-125                                                                                                    -------------------------------------------------------------------------------------------------------KH_5-1l2fA01 A:229-297                                               ----------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....eeeee......eeeeee.ee.........eehhhhhhh...........eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee...eeeeee..eeeeee.hhh..........eeeeeeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeee.....hhhhhhhh..hhhhhhhhhhh...eeeeee...hhhhhhhhhh......eee.......eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2f A   1 mNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVmGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLmKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDPNVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPImNL 344
                            |       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       310       320       330       340 |  
                            |                                                                                                                                              146-MSE                                                       208-MSE                                                                                                                               342-MSE
                            1-MSE
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: KH (43)
(-)
Clan: no clan defined [family: NusA_N] (3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X298_THEMA | Q9X298)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0031554    regulation of DNA-templated transcription, termination    Any process that modulates the frequency, rate, extent, or location of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031564    transcription antitermination    Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9X298_THEMA | Q9X298: 1hh2

(-) Related Entries Specified in the PDB File

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