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(-) Description

Title :  NUCLEOTIDE BINDING DOMAIN OF HUMAN ABCB6 (ADP MG BOUND STRUCTURE)
 
Authors :  M. Haffke, A. Menzel, Y. Carius, D. Jahn, D. W. Heinz
Date :  14 Jun 10  (Deposition) - 25 Aug 10  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Abc-Transporter, Abcb6, Nucleotide Binding Domain, Heme Biosynthesis, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Haffke, A. Menzel, Y. Carius, D. Jahn, D. W. Heinz
Structures Of The Nucleotide-Binding Domain Of The Human Abcb6 Transporter And Its Complexes With Nucleotides.
Acta Crystallogr. , Sect. D V. 66 979 2010
PubMed-ID: 20823549  |  Reference-DOI: 10.1107/S0907444910028593

(-) Compounds

Molecule 1 - ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 6, MITOCHONDRIAL
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainTUNER (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNUCLEOTIDE BINDING DOMAIN OF THE HUMAN ACB-TRANSPORTER ABCB6
    GeneABCB6, MTABC3, PRP, UMAT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITOCHONDRIAL ABC TRANSPORTER 3, MT-ABC TRANSPORTER 3, UBIQUITOUSLY-EXPRESSED MAMMALIAN ABC HALF TRANSPORTER, P- GLYCOPROTEIN-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3MG1Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:113 , LEU A:750 , LEU A:769 , CYS A:773 , THR A:787BINDING SITE FOR RESIDUE PO4 A 1
2AC2SOFTWAREMG A:3 , HOH A:48 , HOH A:105 , HOH A:133 , GLU A:562 , TYR A:599 , THR A:605 , GLY A:626 , ALA A:627 , GLY A:628 , LYS A:629 , SER A:630 , THR A:631BINDING SITE FOR RESIDUE ADP A 2
3AC3SOFTWAREADP A:2 , HOH A:48 , HOH A:78 , HOH A:105 , HOH A:133 , GLU A:562BINDING SITE FOR RESIDUE MG A 3
4AC4SOFTWAREPHE A:639BINDING SITE FOR RESIDUE BME A 4
5AC5SOFTWAREILE A:666 , GLY A:667 , VAL A:668 , LYS A:743BINDING SITE FOR RESIDUE BME A 5

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NHA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NHA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070604G579EABCB6_HUMANDisease (DUH3)397514758AG579E
2UniProtVAR_029749R648QABCB6_HUMANPolymorphism13402964AR648Q
3UniProtVAR_076206R723QABCB6_HUMANDisease (PSHK2)148211042AR723Q
4UniProtVAR_067395L811VABCB6_HUMANDisease (MCOPCB7)387906910AL811V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TRANSPORTER_1PS00211 ABC transporters family signature.ABCB6_HUMAN727-741  1A:727-741

(-) Exons   (0, 0)

(no "Exon" information available for 3NHA)

(-) 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:278
 aligned with ABCB6_HUMAN | Q9NP58 from UniProtKB/Swiss-Prot  Length:842

    Alignment length:299
                                   539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819         
          ABCB6_HUMAN   530 YVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEETEVKDLPGAGPLRFQKGRIEFENVHFSYADGRETLQDVSFTVMPGQTLALVGPSGAGKSTILRLLFRFYDISSGCIRIDGQDISQVTQASLRSHIGVVPQDTVLFNDTIADNIRYGRVTAGNDEVEAAAQAAGIHDAIMAFPEGYRTQVGERGLKLSGGEKQRVAIARTILKAPGIILLDEATSALDTSNERAIQASLAKVCANRTTIVVAHRLSTVVNADQILVIKDGCIVERGRHEALLSRGGVYADMWQLQQGQ 828
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------ABC_tran-3nhaA01 A:630-755                                                                                                    ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh--------------------hhhhhhhhhhh.....................eeeeeeee....-...eeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee.hhhhhhhhhhheeee........eehhhhhhh.....hhhhhhhhhhhh.hhhhhhh..hhhh.ee.......hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------E--------------------------------------------------------------------Q--------------------------------------------------------------------------Q---------------------------------------------------------------------------------------V----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nha A 550 LVPRGSHM--------------------FIDMENMFDLLKEETEVKDLPGAGPLRFQKGRIEFENVHFSYAD-RETLQDVSFTVMPGQTLALVGPSGAGKSTILRLLFRFYDISSGCIRIDGQDISQVTQASLRSHIGVVPQDTVLFNDTIADNIRYGRVTAGNDEVEAAAQAAGIHDAIMAFPEGYRTQVGERGLKLSGGEKQRVAIARTILKAPGIILLDEATSALDTSNERAIQASLAKVCANRTTIVVAHRLSTVVNADQILVIKDGCIVERGRHEALLSRGGVYADMWQLQQGQ 828
                                   | -         -       559       569       579       589       599 | |   609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819         
                                 557                  558                                        601 |                                                                                                                                                                                                                                 
                                                                                                   603                                                                                                                                                                                                                                 

   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 3NHA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NHA)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ABCB6_HUMAN | Q9NP58)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0015562    efflux transmembrane transporter activity    Enables the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0015232    heme transporter activity    Enables the directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells.
    GO:0015439    heme-transporting ATPase activity    Catalysis of the reaction: ATP + H2O + heme(in) = ADP + phosphate + heme(out).
    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.
biological process
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0015886    heme transport    The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    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:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0031307    integral component of mitochondrial outer membrane    The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ABCB6_HUMAN | Q9NP583nh6 3nh9 3nhb

(-) Related Entries Specified in the PDB File

3nh6 THE SAME PROTEIN IN THE APO FORM
3nh9 THE SAME PROTEIN IN THE ATP BOUND FORM
3nhb THE SAME PROTEIN IN THE ADP BOUND FORM