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(-) Description

Title :  SOLUTION STRUCTURE OF THE COPPER(I) FORM OF THE FIFTH DOMAIN OF MENKES PROTEIN
 
Authors :  L. Banci, C. T. Chasapis, S. Ciofi-Baffoni, N. Hadjiliadis, A. Rosato, Structural Proteomics In Europe (Spine)
Date :  25 Nov 04  (Deposition) - 08 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ferrodoxin-Like Fold, Beta-Alpha-Beta-Beta-Alpha-Beta Structure, Structural Proteomics In Europe, Spine, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Banci, I. Bertini, S. Ciofi-Baffoni, C. T. Chasapis, N. Hadjiliadis, A. Rosato
An Nmr Study Of The Interaction Between The Human Copper(I) Chaperone And The Second And Fifth Metal-Binding Domains Of The Menkes Protein
Febs J. V. 272 865 2005
PubMed-ID: 15670166  |  Reference-DOI: 10.1111/J.1742-4658.2004.04526.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER-TRANSPORTING ATPASE 1
    ChainsA
    EC Number3.6.3.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20B(+)
    Expression System StrainBL21(DE3)PLYS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFIFTH DOMAIN OF THE MENKES PROTEIN
    GeneATP7A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMENKES PROTEIN, COPPER PUMP 1, MENKES DISEASE- ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:14 , ALA A:15 , CYS A:17BINDING SITE FOR RESIDUE CU A 78

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y3J)

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMA_2PS50846 Heavy-metal-associated domain profile.ATP7A_HUMAN9-75
172-238
278-344
378-444
489-555
565-631
  2-
-
-
-
A:4-70
A:77-77
2HMA_1PS01047 Heavy-metal-associated domain.ATP7A_HUMAN14-43
177-206
283-312
383-412
494-523
570-599
  2-
-
-
-
A:9-38
A:77-77

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003415141bENSE00001863720X:77166199-77166332134ATP7A_HUMAN-00--
1.5bENST000003415145bENSE00002166326X:77227118-77227258141ATP7A_HUMAN1-40400--
1.6bENST000003415146bENSE00001636041X:77243738-77244227490ATP7A_HUMAN41-2041640--
1.7ENST000003415147ENSE00002161973X:77244729-77245454726ATP7A_HUMAN204-4462430--
1.8ENST000003415148ENSE00001712655X:77253975-77254181207ATP7A_HUMAN446-515701A:1-3030
1.9ENST000003415149ENSE00001656404X:77258570-77258733164ATP7A_HUMAN515-569551A:30-76 (gaps)48
1.10ENST0000034151410ENSE00001633722X:77264599-77264760162ATP7A_HUMAN570-623540--
1.11ENST0000034151411ENSE00001690695X:77266673-7726674977ATP7A_HUMAN624-649260--
1.12bENST0000034151412bENSE00001735395X:77266946-77267171226ATP7A_HUMAN649-724760--
1.14ENST0000034151414ENSE00001628072X:77268376-77268609234ATP7A_HUMAN725-802780--
1.15ENST0000034151415ENSE00001765102X:77270159-7727025092ATP7A_HUMAN803-833310--
1.16ENST0000034151416ENSE00001791031X:77271251-77271378128ATP7A_HUMAN833-876440--
1.17ENST0000034151417ENSE00001694839X:77275741-77275895155ATP7A_HUMAN876-927520--
1.18ENST0000034151418ENSE00001625459X:77276442-77276576135ATP7A_HUMAN928-972450--
1.19ENST0000034151419ENSE00001594340X:77284747-77284941195ATP7A_HUMAN973-1037650--
1.20ENST0000034151420ENSE00001760012X:77286898-77287080183ATP7A_HUMAN1038-1098610--
1.21ENST0000034151421ENSE00001673903X:77289103-77289319217ATP7A_HUMAN1099-1171730--
1.22bENST0000034151422bENSE00001683584X:77294334-77294480147ATP7A_HUMAN1171-1220500--
1.24ENST0000034151424ENSE00001729880X:77296089-77296231143ATP7A_HUMAN1220-1267480--
1.25ENST0000034151425ENSE00001626594X:77298083-77298286204ATP7A_HUMAN1268-1335680--
1.26ENST0000034151426ENSE00001621294X:77298815-77298932118ATP7A_HUMAN1336-1375400--
1.27aENST0000034151427aENSE00001671536X:77300967-77301069103ATP7A_HUMAN1375-1409350--
1.28ENST0000034151428ENSE00001091570X:77301791-773058924102ATP7A_HUMAN1409-1500920--

(-) 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:77
 aligned with ATP7A_HUMAN | Q04656 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:86
                                   495       505       515       525       535       545       555       565      
          ATP7A_HUMAN   486 NSSKCYIQVTGMTCASCVANIERNLRREEGIYSILVALMAGKAEVRYNPAVIQPPMIAEFIRELGFGATVIENADEGDGVLELVVR 571
               SCOP domains d1y3ja_ A: automated matches                                                           SCOP domains
               CATH domains 1y3jA00 A:1-77  [code=3.30.70.100, no name defined]                                    CATH domains
               Pfam domains -----HMA-1y3jA01 A:6-67                                            ------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhh....eee.........eeeee.....hhhhhhhhhhhhh..eeee...-..--------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HMA_2  PDB: A:4-70 UniProt: 489-555                                ---------HMA_2   PROSITE (1)
                PROSITE (2) --------HMA_1  PDB: A:9-38            ----------------------------------------------HM PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: A:1-30         ------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.9  PDB: A:30-76 (gaps) UniProt: 515-569         -- Transcript 1 (2)
                 1y3j A   1 NSSKCYIQVTGMTCASCVANIERNLRREEGIYSILVALMAGKAEVRYNPAVIQPPMIAEFIRELGFGATVIENI-EG--------R  77
                                    10        20        30        40        50        60        70   | ||  -     |
                                                                                                    74 ||       77
                                                                                                      75|         
                                                                                                       76         

   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  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (74, 74)

NMR Structure(hide GO term definitions)
Chain A   (ATP7A_HUMAN | Q04656)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019829    cation-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0005375    copper ion transmembrane transporter activity    Catalysis of the transfer of copper (Cu) ions from one side of a membrane to the other.
    GO:0032767    copper-dependent 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), in the presence of copper.
    GO:0004008    copper-exporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Cu2+(in) -> ADP + phosphate + Cu2+(out).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0016532    superoxide dismutase copper chaperone activity    A copper chaperone activity that specifically delivers copper to the Cu-Zn superoxide dismutase, to activate superoxide dismutase activity.
biological process
    GO:0042093    T-helper cell differentiation    The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell.
    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:0001974    blood vessel remodeling    The reorganization or renovation of existing blood vessels.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0006584    catecholamine metabolic process    The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0021954    central nervous system neuron development    The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
    GO:0021702    cerebellar Purkinje cell differentiation    The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem.
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0060003    copper ion export    The directed movement of copper ions out of a cell or organelle.
    GO:0015677    copper ion import    The directed movement of copper ions into a cell or organelle.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010273    detoxification of copper ion    Any process that reduces or removes the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion.
    GO:0042417    dopamine metabolic process    The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
    GO:0048251    elastic fiber assembly    Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.
    GO:0051542    elastin biosynthetic process    The chemical reactions and pathways resulting in the formation of elastin, a fibrous glycoprotein found in elastic tissues such as the walls of arteries.
    GO:0042414    epinephrine metabolic process    The chemical reactions and pathways involving epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0031069    hair follicle morphogenesis    The process in which the anatomical structures of the hair follicle are generated and organized.
    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:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    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:0048286    lung alveolus development    The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0042415    norepinephrine metabolic process    The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
    GO:0018205    peptidyl-lysine modification    The modification of peptidyl-lysine.
    GO:0043473    pigmentation    The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
    GO:0015679    plasma membrane copper ion transport    The directed movement of copper ions across the plasma membrane.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0051353    positive regulation of oxidoreductase activity    Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
    GO:0021860    pyramidal neuron development    The progression of a pyramidal neuron from its initial formation to its mature state.
    GO:0002082    regulation of oxidative phosphorylation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0046688    response to copper 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 copper ion stimulus.
    GO:0010041    response to iron(III) 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 an iron(III) ion stimulus.
    GO:0010043    response to zinc 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 zinc ion stimulus.
    GO:0042428    serotonin metabolic process    The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    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.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0030140    trans-Golgi network transport vesicle    A vesicle that mediates transport between the trans-Golgi network and other parts of the cell.

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  ATP7A_HUMAN | Q04656
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 Related Entries

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

UniProtKB/Swiss-Prot
        ATP7A_HUMAN | Q046561aw0 1kvi 1kvj 1q8l 1s6o 1s6u 1y3k 1yjr 1yjt 1yju 1yjv 2aw0 2g9o 2ga7 2k1r 2kij 2kmv 2kmx 3cjk 5t7l

(-) Related Entries Specified in the PDB File

1y3k THE SAME PROTEIN OF THE APO FORM RELATED ID: CIRMMP26 RELATED DB: TARGETDB