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(-) Description

Title :  SOLUTION STRUCTURE OF MLL CXXC DOMAIN IN COMPLEX WITH PALINDROMIC CPG DNA
 
Authors :  T. Cierpicki, J. E. Riesbeck, J. E. Grembecka, S. M. Lukasik, R. Popovic, M. Omonkowska, D. S. Shultis, N. J. Zeleznik-Le, J. H. Bushweller
Date :  18 Jun 09  (Deposition) - 08 Dec 09  (Release) - 19 Jan 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
Keywords :  Protein-Dna Complex, Cxxc Domain, Mll, Cpg Dna, Chromosomal Rearrangement, Dna-Binding, Metal-Binding, Nucleus, Zinc- Finger, Dna Binding Protein/Dna Complex, Alternative Splicing, Apoptosis, Bromodomain, Chromatin Regulator, Isopeptide Bond, Methyltransferase, Phosphoprotein, Polymorphism, Proto-Oncogene, S-Adenosyl-L-Methionine, Transcription, Transcription Regulation, Transferase, Ubl Conjugation, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Cierpicki, L. E. Risner, J. Grembecka, S. M. Lukasik, R. Popovic, M. Omonkowska, D. D. Shultis, N. J. Zeleznik-Le, J. H. Bushweller
Structure Of The Mll Cxxc Domain-Dna Complex And Its Functional Role In Mll-Af9 Leukemia.
Nat. Struct. Mol. Biol. V. 17 62 2010
PubMed-ID: 20010842  |  Reference-DOI: 10.1038/NSMB.1714
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE HRX
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4-T2
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCXXC DOMAIN: UNP RESIDUES 1147-1203
    GeneALL1, CXXC7, HRX, HTRX, KMT2A, MLL, TRX1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZINC FINGER PROTEIN HRX, ALL-1, TRITHORAX-LIKE PROTEIN, LYSINE N-METHYLTRANSFERASE 2A, CXXC-TYPE ZINC FINGER PROTEIN 7
 
Molecule 2 - 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'
    ChainsB, C
    EngineeredYES
    Other DetailsPALINDROMIC DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1155 , GLY A:1156 , CYS A:1158 , CYS A:1161 , CYS A:1194BINDING SITE FOR RESIDUE ZN A 2001
2AC2SOFTWARECYS A:1167 , CYS A:1170 , CYS A:1173 , CYS A:1189BINDING SITE FOR RESIDUE ZN A 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KKF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KKF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KKF)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CXXCPS51058 Zinc finger CXXC-type profile.KMT2A_HUMAN1147-1195  1A:1147-1195

(-) Exons   (0, 0)

(no "Exon" information available for 2KKF)

(-) 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:57
 aligned with KMT2A_HUMAN | Q03164 from UniProtKB/Swiss-Prot  Length:3969

    Alignment length:57
                                  1156      1166      1176      1186      1196       
         KMT2A_HUMAN   1147 KKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKCQNLQWMPSK 1203
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh......hhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_CXXC  PDB: A:1147-1195 UniProt: 1147-1195     -------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                2kkf A 1147 KKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKCQNLQWMPSK 1203
                                  1156      1166      1176      1186      1196       

Chain B from PDB  Type:DNA  Length:12
                                             
                2kkf B  101 CCCTGCGCAGGG  112
                                   110  

Chain C from PDB  Type:DNA  Length:12
                                             
                2kkf C  101 CCCTGCGCAGGG  112
                                   110  

   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  (0, 0)

(no "SCOP Domain" information available for 2KKF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KKF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KKF)

(-) Gene Ontology  (60, 60)

NMR Structure(hide GO term definitions)
Chain A   (KMT2A_HUMAN | Q03164)
molecular function
    GO:0003680    AT DNA binding    Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0001046    core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0045322    unmethylated CpG binding    Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0050890    cognition    The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
    GO:0060216    definitive hemopoiesis    A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood.
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0035640    exploration behavior    The specific behavior of an organism in response to a novel environment or stimulus.
    GO:0044648    histone H3-K4 dimethylation    The modification of histone H3 by addition of two methyl groups to lysine at position 4 of the histone.
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0080182    histone H3-K4 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0048873    homeostasis of number of cells within a tissue    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
    GO:0051899    membrane depolarization    The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    GO:2001040    positive regulation of cellular response to drug    Any process that activates or increases the frequency, rate or extent of cellular response to drug.
    GO:0051571    positive regulation of histone H3-K4 methylation    Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0032411    positive regulation of transporter activity    Any process that activates or increases the activity of a transporter.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0071440    regulation of histone H3-K14 acetylation    Any process that modulates the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
    GO:1901674    regulation of histone H3-K27 acetylation    Any process that modulates the frequency, rate or extent of histone H3-K27 acetylation.
    GO:0051569    regulation of histone H3-K4 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:2000615    regulation of histone H3-K9 acetylation    Any process that modulates the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0048172    regulation of short-term neuronal synaptic plasticity    A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009416    response to light stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0035864    response to potassium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        KMT2A_HUMAN | Q031642agh 2j2s 2jyi 2ku7 2kyu 2lxs 2lxt 2msr 2mtn 2w5y 2w5z 3eg6 3emh 3lqh 3lqi 3lqj 3p4f 3u85 3u88 4esg 4gq6 4nw3 5f5e 5f6l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KKF)