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(-) Description

Title :  CRYSTAL STRUCTURE OF TOLLOID-LIKE PROTEASE 1 (TLL-1) PROTEASE DOMAIN
 
Authors :  A. Mac Sweeney
Date :  03 Sep 08  (Deposition) - 16 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Disordered Cysteine-Rich Loop, Alternative Splicing, Calcium, Developmental Protein, Differentiation, Egf-Like Domain, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Polymorphism, Protease, Secreted, 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 - TOLLOID-LIKE PROTEIN 1
    ChainsA
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPROTEASE DOMAIN
    GeneTLL1, TLL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTLL-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3SO43Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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
2AC2SOFTWARECYS A:65 , HIS A:92 , HIS A:96 , HIS A:102BINDING SITE FOR RESIDUE ZN A 210
3AC3SOFTWAREGLU A:103 , GLN A:189 , HOH A:236 , HOH A:240 , HOH A:247BINDING SITE FOR RESIDUE ZN A 211
4AC4SOFTWAREHIS A:36 , LYS A:39 , HIS A:40BINDING SITE FOR RESIDUE SO4 A 212
5AC5SOFTWARESER A:4 , ARG A:5 , THR A:6 , ARG A:151 , HOH A:258 , HOH A:287 , HOH A:362 , HOH A:370BINDING SITE FOR RESIDUE SO4 A 213
6AC6SOFTWARESER A:167 , ARG A:168 , ARG A:170 , HOH A:279 , HOH A:437BINDING SITE FOR RESIDUE SO4 A 214
7AC7SOFTWARETYR A:17 , LYS A:31 , ARG A:35 , GLU A:38 , PHE A:45 , HOH A:414BINDING SITE FOR RESIDUE DMS A 215

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:198

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_062519M182LTLL1_HUMANDisease (ASD6)137852951AM34L
2UniProtVAR_062520V238ATLL1_HUMANDisease (ASD6)137852952AV90A

  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.TLL1_HUMAN237-246  1A:89-98

(-) Exons   (0, 0)

(no "Exon" information available for 3EDI)

(-) 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:196
 aligned with TLL1_HUMAN | O43897 from UniProtKB/Swiss-Prot  Length:1013

    Alignment length:202
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
          TLL1_HUMAN    148 AATSRTERIWPGGVIPYVIGGNFTGSQRAMFKQAMRHWEKHTCVTFIERSDEESYIVFTYRPCGCCSYVGRRGNGPQAISIGKNCDKFGIVVHELGHVIGFWHEHTRPDRDNHVTIIRENIQPGQEYNFLKMEPGEVNSLGERYDFDSIMHYARNTFSRGMFLDTILPSRDDNGIRPAIGQRTRLSKGDIAQARKLYRCPAC  349
               SCOP domains d3edia_ A: automated matches                                                                                                                                                                               SCOP domains
               CATH domains 3ediA00 A:1-200 Collagenase (Catalytic Domain)                                                                                                                                                           - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhh..eeee.......eeee..----...........eeee.--...hhhhhhhhhhhhhh..hhhhh.hhhh.eee.hhhh...hhhhhh..hhhhh............................eee.................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------L-------------------------------------------------------A--------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3edi A    1 AATSRTERIWPGGVIPYVIGGNFTGSQRAMFKQAMRHWEKHTCVTFIERSDEESYIVFTYR----CSYVGRRGNGPQAISI--NCDKFGIVVHELGHVIGFWHEHTRPDRDNHVTIIRENIQPGQEYNFLKMEPGEVNSLGERYDFDSIMHYARNTFSRGMFLDTILPSRDDNGIRPAIGQRTRLSKGDIAQARKLYRCPAx  201
                                    10        20 |      29        39        49        59|    |  69   |    78|  |    89        99       109       119       129   ||  137       147       157|      168||||   174 ||    187       199 |
                                               21A                                     60   65     72A     79 83                                              132A|                      157|      168A|||     176|            195|  |
                                                                                                                                                               132B                       159       168B||      180             198  |
                                                                                                                                                                                                     168C|                         201-ACE
                                                                                                                                                                                                      168D                            

   Legend:   → Mismatch (orange background)
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  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 3EDI)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TLL1_HUMAN | O43897)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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: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.

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