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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF BONE MORPHOGENETIC PROTEIN-6 (BMP-6)
 
Authors :  T. D. Mueller, W. Sebald, S. Saremba
Date :  03 Sep 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bmp-6, Tgf-Beta Ligand, Chondrogenesis, Cleavage On Pair Of Basic Residues, Cytokine, Developmental Protein, Differentiation, Glycoprotein, Growth Factor, Osteogenesis, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Saremba, J. Nickel, A. Seher, A. Kotzsch, W. Sebald, T. D. Mueller
Type I Receptor Binding Of Bone Morphogenetic Protein 6 Is Dependent On N-Glycosylation Of The Ligand.
Febs J. V. 275 172 2007
PubMed-ID: 18070108  |  Reference-DOI: 10.1111/J.1742-4658.2007.06187.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BONE MORPHOGENETIC PROTEIN 6
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPN25
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentMATURE PART (RESIDUES 375-513)
    GeneBMP6, VGR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP-6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1IPA10Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:76BINDING SITE FOR RESIDUE IPA B 133
02AC2SOFTWARELYS A:119 , LYS A:120 , TYR A:121 , ARG A:122 , ASN B:76BINDING SITE FOR RESIDUE IPA A 133
03AC3SOFTWAREASN B:69 , ASN B:113 , ASN B:115BINDING SITE FOR RESIDUE IPA B 134
04AC4SOFTWARETRP A:45 , TYR A:109 , TYR A:121 , LYS B:53BINDING SITE FOR RESIDUE IPA B 135
05AC5SOFTWAREASP A:42 , LEU A:43 , SER B:106BINDING SITE FOR RESIDUE IPA B 136
06AC6SOFTWAREASN B:103 , ALA B:104BINDING SITE FOR RESIDUE IPA B 137
07AC7SOFTWAREASN A:103 , ALA A:104 , LYS A:120BINDING SITE FOR RESIDUE IPA A 134
08AC8SOFTWAREARG A:32 , HIS A:34 , GLU A:35BINDING SITE FOR RESIDUE IPA A 135
09AC9SOFTWAREALA A:51 , PRO A:52BINDING SITE FOR RESIDUE IPA A 136
10BC1SOFTWAREASN A:76 , ILE A:79BINDING SITE FOR RESIDUE IPA A 137

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:97
2A:60 -A:129
3A:64 -A:131
4A:96 -B:96
5B:31 -B:97
6B:60 -B:129
7B:64 -B:131

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:51 -Pro A:52
2Phe A:66 -Pro A:67
3Ala B:51 -Pro B:52
4Phe B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036201P476LBMP6_HUMANUnclassified  ---A/BP95L

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.BMP6_HUMAN430-445
 
  2A:49-64
B:49-64

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002831471ENSE00001009161chr6:7727030-7727852823BMP6_HUMAN1-2222220--
1.2ENST000002831472ENSE00001083364chr6:7845373-7845565193BMP6_HUMAN222-286650--
1.3ENST000002831473ENSE00001154874chr6:7861684-7861832149BMP6_HUMAN286-336510--
1.4ENST000002831474ENSE00001083374chr6:7862534-7862731198BMP6_HUMAN336-402670--
1.5ENST000002831475ENSE00001154858chr6:7879307-787938377BMP6_HUMAN402-427262A:28-46
B:28-46
19
19
1.6ENST000002831476ENSE00001154849chr6:7880224-7880334111BMP6_HUMAN428-464372A:47-83
B:47-83
37
37
1.7ENST000002831477ENSE00001258022chr6:7880427-78816551229BMP6_HUMAN465-513492A:84-132
B:84-132
49
49

(-) 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:105
 aligned with BMP6_HUMAN | P22004 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:105
                                   418       428       438       448       458       468       478       488       498       508     
           BMP6_HUMAN   409 KTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 513
               SCOP domains d2r52a_ A: automated matches                                                                              SCOP domains
               CATH domains 2r52A00 A:28-132 Cystine-knot cytokines                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....hhh.eee..eee..eee.............hhhhhhhhhhhhh........eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------L------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.5           Exon 1.6  PDB: A:47-83               Exon 1.7  PDB: A:84-132 UniProt: 465-513          Transcript 1
                 2r52 A  28 KTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 132
                                    37        47        57        67        77        87        97       107       117       127     

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with BMP6_HUMAN | P22004 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:105
                                   418       428       438       448       458       468       478       488       498       508     
           BMP6_HUMAN   409 KTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 513
               SCOP domains d2r52b_ B: automated matches                                                                              SCOP domains
               CATH domains 2r52B00 B:28-132 Cystine-knot cytokines                                                                   CATH domains
           Pfam domains (1) TGF_beta-2r52B01 B:28-132                                                                                 Pfam domains (1)
           Pfam domains (2) TGF_beta-2r52B02 B:28-132                                                                                 Pfam domains (2)
         Sec.struct. author ....eee..eee.........eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh.......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------L------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.5           Exon 1.6  PDB: B:47-83               Exon 1.7  PDB: B:84-132 UniProt: 465-513          Transcript 1
                 2r52 B  28 KTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 132
                                    37        47        57        67        77        87        97       107       117       127     

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BMP6_HUMAN | P22004)
molecular function
    GO:0070700    BMP receptor binding    Interacting selectively and non-covalently with a BMP receptor.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    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:0071773    cellular response to BMP 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 bone morphogenetic protein (BMP) stimulus.
    GO:0071281    cellular response to iron ion    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 an iron ion stimulus.
    GO:0071260    cellular response to mechanical 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 mechanical stimulus.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0030539    male genitalia development    The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0060586    multicellular organismal iron ion homeostasis    Any process involved in the maintenance of the distribution of iron stores within tissues and organs of a multicellular organism.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:2000105    positive regulation of DNA-dependent DNA replication    Any process that activates or increases the frequency, rate or extent of DNA-dependent DNA replication.
    GO:0060391    positive regulation of SMAD protein import into nucleus    Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0032349    positive regulation of aldosterone biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone.
    GO:2000860    positive regulation of aldosterone secretion    Any process that activates or increases the frequency, rate or extent of aldosterone secretion.
    GO:0030501    positive regulation of bone mineralization    Any process that activates or increases the frequency, rate or extent of bone mineralization.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:0045603    positive regulation of endothelial cell differentiation    Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0031666    positive regulation of lipopolysaccharide-mediated signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    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:0043408    regulation of MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0014823    response to activity    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 activity stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0010039    response to iron 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 ion stimulus.
    GO:0032026    response to magnesium 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 magnesium ion stimulus.
    GO:0032526    response to retinoic acid    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 retinoic acid stimulus.
    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:0003323    type B pancreatic cell development    The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BMP6_HUMAN | P220042qcw 2r53

(-) Related Entries Specified in the PDB File

1rew BINARY COMPLEX OF BMP-2 BOUND TO ITS TYPE I RECEPTOR BMPR-IA
2h62 TERNARY COMPLEX OF BMP-2 BOUND TO ITS TYPE I RECEPTOR BMPR- IA AND ITS TYPE II RECEPTOR ACTR-IIB
2h64 TERNARY COMPLEX OF A BMP-2 VARIANT BOUND TO ITS TYPE I RECEPTOR BMPR-IA AND ITS TYPE II RECEPTOR ACTR-IIB
2r53
3bmp BMP-2 LIGAND STRUCTURE