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(-) Description

Title :  SOLUTION STRUCTURE OF THE SEQUENCE-NON-SPECIFIC HMGB PROTEIN NHP6A
 
Authors :  J. E. Masse, B. Wong, Y. -M. Yen, F. H. -T. Allain, R. C. Johnson, J. Feigon
Date :  31 May 02  (Deposition) - 16 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hmg-Box, Hmgb, Alpha Helix, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Masse, B. Wong, Y. -M. Yen, F. H. -T. Allain, R. C. Johnson, J. Feigon
The S. Cerevisiae Architectural Hmgb Protein Nhp6A Complexed With Dna: Dna And Protein Conformational Changes Upon Binding
J. Mol. Biol. V. 323 263 2002
PubMed-ID: 12381320  |  Reference-DOI: 10.1016/S0022-2836(02)00938-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NONHISTONE CHROMOSOMAL PROTEIN 6A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NHP6A
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: NHP6A

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LWM)

(-) Sites  (0, 0)

(no "Site" information available for 1LWM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.NHP6A_YEAST21-89  1A:21-89

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR052C1YPR052C.1XVI:665971-665690282NHP6A_YEAST1-93931A:1-9393

(-) Sequences/Alignments

NMR Structure
   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:93
 aligned with NHP6A_YEAST | P11632 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
           NHP6A_YEAST    1 MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93
               SCOP domains d1lwma_ A: NHP6a                                                                              SCOP domains
               CATH domains 1lwmA00 A:1-93 DNA Binding (I), subunit A                                                     CATH domains
               Pfam domains --------------------HMG_box-1lwmA01 A:21-89                                              ---- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------HMG_BOX_2  PDB: A:21-89 UniProt: 21-89                               ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-93 UniProt: 1-93                                                           Transcript 1
                  1lwm A  1 MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93
                                    10        20        30        40        50        60        70        80        90
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (NHP6A_YEAST | P11632)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0034724    DNA replication-independent nucleosome organization    The formation or destruction of chromatin structures, occurring outside the context of DNA replication.
    GO:0051123    RNA polymerase II transcriptional preinitiation complex assembly    The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
    GO:0070898    RNA polymerase III transcriptional preinitiation complex assembly    The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase III promoter.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0001195    maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter    Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    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.
cellular component
    GO:0032301    MutSalpha complex    A heterodimer involved in the recognition and repair of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MSH2 and MSH6.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  NHP6A_YEAST | P11632
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 Related Entries

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

UniProtKB/Swiss-Prot
        NHP6A_YEAST | P11632: 1cg7 1j5n

(-) Related Entries Specified in the PDB File

1cg7 FREE NHP6A PROTEIN STRUCTURE (1999)
1j5n NHP6A/SRY_DNA COMPLEX
1lwa FREE SRY_DNA STRUCTURE