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(-) Description

Title :  CRYSTAL STRUCTURE OF BONE MORPHOGENETIC PROTEIN 1 PROTEASE DOMAIN IN COMPLEX WITH PARTIALLY BOUND DMSO
 
Authors :  A. Mac Sweeney
Date :  03 Sep 08  (Deposition) - 16 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Vicinal Disulfide, Alternative Splicing, Calcium, Chondrogenesis, Cleavage On Pair Of Basic Residues, Cytokine, Developmental Protein, Differentiation, Egf-Like Domain, Glycoprotein, Growth Factor, Hydrolase, Metal- Binding, Metalloprotease, Osteogenesis, Polymorphism, Protease, Zinc, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Mac Sweeney, S. G. Parrado, D. Vinzenz, A. Bernardi, A. Hein, U. Bodendorf, P. Erbel, C. Logel, B. Gerhartz
Structural Basis For The Substrate Specificity Of Bone Morphogenetic Protein 1/Tolloid-Like Metalloproteases
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BONE MORPHOGENETIC PROTEIN 1
    ChainsA
    EC Number3.4.24.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPROTEASE DOMAIN
    GeneBMP1, PCOLC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP-1, PROCOLLAGEN C-PROTEINASE, PCP, MAMMALIAN TOLLOID PROTEIN, MTLD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DMS5Ligand/IonDIMETHYL SULFOXIDE
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:1 , ALA A:2 , GLU A:103 , ARG A:106 , SER A:136 , GLN A:189BINDING SITE FOR RESIDUE ACE A 201
2AC2SOFTWAREHIS A:92 , HIS A:96 , HIS A:102BINDING SITE FOR RESIDUE ZN A 210
3AC3SOFTWAREGLU A:103 , GLN A:189 , HOH A:221 , HOH A:224 , HOH A:228BINDING SITE FOR RESIDUE ZN A 211
4AC4SOFTWARELYS A:39 , HIS A:40 , ARG A:106 , ASP A:108 , GLU A:139 , HOH A:290 , HOH A:581BINDING SITE FOR RESIDUE DMS A 212
5AC5SOFTWAREARG A:35 , LYS A:39 , LYS A:192 , HOH A:462 , HOH A:594BINDING SITE FOR RESIDUE DMS A 213
6AC6SOFTWARECYS A:64 , HIS A:92 , GLU A:93 , HIS A:96 , HIS A:102 , HOH A:297 , HOH A:306 , HOH A:314 , HOH A:604 , HOH A:609BINDING SITE FOR RESIDUE DMS A 214
7AC7SOFTWAREASP A:50 , ARG A:176 , THR A:180 , HOH A:536BINDING SITE FOR RESIDUE DMS A 215
8AC8SOFTWAREARG A:31 , GLU A:38 , PHE A:45 , HOH A:546BINDING SITE FOR RESIDUE DMS A 216

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:198
2A:62 -A:84
3A:64 -A:65

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:64 -Cys A:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067224F249LBMP1_HUMANDisease (OI13)398122891AF128L
2UniProtVAR_072248M270VBMP1_HUMANDisease (OI13)786205219AM147V

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.BMP1_HUMAN210-219  1A:89-98

(-) Exons   (0, 0)

(no "Exon" information available for 3EDH)

(-) 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:202
 aligned with BMP1_HUMAN | P13497 from UniProtKB/Swiss-Prot  Length:986

    Alignment length:202
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
          BMP1_HUMAN    121 AATSRPERVWPDGVIPFVIGGNFTGSQRAVFRQAMRHWEKHTCVTFLERTDEDSYIVFTYRPCGCCSYVGRRGGGPQAISIGKNCDKFGIVVHELGHVVGFWHEHTRPDRDRHVSIVRENIQPGQEYNFLKMEPQEVESLGETYDFDSIMHYARNTFSRGIFLDTIVPKYEVNGVKPPIGQRTRLSKGDIAQARKLYKCPAC  322
               SCOP domains d3edha_ A: automated matches                                                                                                                                                                               SCOP domains
               CATH domains 3edhA00 A:1-200 Collagenase (Catalytic Domain)                                                                                                                                                           - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhh..eeee......eeeeee...............eeeeeehhhhhhhhhhhhhhhhhhh..hhhhh.hhhh.eee.hhhh...hhhhhh..hhhhh............................eee.................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------L--------------------V---------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3edh A    1 AATSRPERVWPDGVIPFVIGGNFTGSQRAVFRQAMRHWEKHTCVTFLERTDEDSYIVFTYRPCGCCSYVGRRGGGPQAISIGKNCDKFGIVVHELGHVVGFWHEHTRPDRDRHVSIVRENIQPGQEYNFLKMEPQEVESLGETYDFDSIMHYARNTFSRGIFLDTIVPKYEVNGVKPPIGQRTRLSKGDIAQARKLYKCPAx  201
                                    10        20 |      29        39        49        59        69   |    78||      89        99       109       119       129   ||  137       147       157|      168||||   174 ||    187       199 |
                                               21A                                                 72A     79|                                                132A|                      157|      168A|||     176|            195|  |
                                                                                                            81                                                 132B                       159       168B||      180             198  |
                                                                                                                                                                                                     168C|                         201-ACE
                                                                                                                                                                                                      168D                            

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EDH)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BMP1_HUMAN | P13497)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0001502    cartilage condensation    The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
    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:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    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: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:0061036    positive regulation of cartilage development    Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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: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).
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: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.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BMP1_HUMAN | P134973edg

(-) Related Entries Specified in the PDB File

1dle ASTACIN
3edg BMP-1
3edi HUMAN TLL-1 CATALYTIC DOMAIN