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(-) Description

Title :  SOLUTION STRUCTURES OF THE BRK DOMAINS OF THE HUMAN CHROMO HELICASE DOMAIN 7 AND 8, REVEALS STRUCTURAL SIMILARITY WITH GYF DOMAIN SUGGESTING A ROLE IN PROTEIN INTERACTION
 
Authors :  E. Ab, R. N. De Jong, T. Diercks, J. Xiaoyun, M. Daniels, R. Kaptein, G. E. Folkers
Date :  14 Apr 06  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Protein-Protein Interaction, Phosphorylation, Disease Mutation, Nucleotide-Binding, Transcription Regulation, Transcription Elongation, Chromatin Regulator, Chromatin Remodeling, Helicase, Hydrolase, Brk Domain, Atp-Binding, Dna-Binding, Transcription, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ab, R. N. De Jong, T. Diercks, J. Xiaoyun, M. Daniels, R. Kaptein, G. E. Folkers
Solution Structures Of The Brk Domains Of The Human Chromo Helicase Domain 7 And 8, Reveals Structural Similarity With Gyf Domain Suggesting A Role In Protein Interaction
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHISLIC
    Expression System StrainROSETTA
    Expression System Taxid562
    FragmentBRK, RESIDUES 1801-1860
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
    SynonymATP-DEPENDENT HELICASE CHD7, CHD-7

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CKC)

(-) Sites  (0, 0)

(no "Site" information available for 2CKC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CKC)

(-) Exons   (0, 0)

(no "Exon" information available for 2CKC)

(-) 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:60
 aligned with CHD7_HUMAN | Q9P2D1 from UniProtKB/Swiss-Prot  Length:2997

    Alignment length:60
                                  2572      2582      2592      2602      2612      2622
          CHD7_HUMAN   2563 LDPDTRIPVINLEDGTRLVGEDAPKNKDLVEWLKLHPTYTVDMPSYVPKNADVLFSSFQK 2622
               SCOP domains d2ckca1 A:2563-2622                                          SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee....eee......hhhhhhhhhhhh..eee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                2ckc A 2563 LDPDTRIPVINLEDGTRLVGEDAPKNKDLVEWLKLHPTYTVDMPSYVPKNADVLFSSFQK 2622
                                  2572      2582      2592      2602      2612      2622

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

NMR Structure(hide GO term definitions)
Chain A   (CHD7_HUMAN | Q9P2D1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    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.
    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:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0007512    adult heart development    The process whose specific outcome is the progression of the adult heart over time, from its formation to the mature structure.
    GO:0007628    adult walking behavior    The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
    GO:0048844    artery morphogenesis    The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    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:0021545    cranial nerve development    The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
    GO:0042471    ear morphogenesis    The process in which the anatomical structures of the ear are generated and organized. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
    GO:0035116    embryonic hindlimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
    GO:0060429    epithelium development    The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
    GO:0060324    face development    The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
    GO:0030540    female genitalia development    The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure.
    GO:0048806    genitalia development    The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0060173    limb development    The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0043584    nose development    The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity).
    GO:0042048    olfactory behavior    The behavior of an organism in response to an odor.
    GO:0021772    olfactory bulb development    The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex.
    GO:0021553    olfactory nerve development    The process whose specific outcome is the progression of the olfactory nerve over time, from its formation to the mature structure. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0040018    positive regulation of multicellular organism growth    Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0060123    regulation of growth hormone secretion    Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0048752    semicircular canal morphogenesis    The process in which the anatomical structures of the semicircular canals are generated and organized.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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)

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        CHD7_HUMAN | Q9P2D12v0e 2v0f

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