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(-) Description

Title :  SOLUTION STRUCTURE OF MMP20 COMPLEXED WITH NNGH
 
Authors :  Y. Arendt, L. Banci, I. Bertini, F. Cantini, R. Cozzi, R. Del Conte, L. Gonnelli, Structural Proteomics In Europe (Spine)
Date :  03 Jul 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Mmp-Nngh, Structural Genomics, Structural Proteomics In Europe, Spine, Spine-2, Spine2-Complexes, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Arendt, L. Banci, I. Bertini, F. Cantini, R. Cozzi, R. Del Conte, L. Gonnelli
Catalytic Domain Of Mmp20 (Enamelysin) - The Nmr Structure Of A New Matrix Metalloproteinase.
Febs Lett. V. 581 4723 2007
PubMed-ID: 17869250  |  Reference-DOI: 10.1016/J.FEBSLET.2007.08.069
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-20
    ChainsA
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 113-272
    GeneMMP20
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMMP-20, ENAMEL METALLOPROTEINASE, ENAMELYSIN
    TissueODONTOBLAST

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

NMR Structure (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NGH1Ligand/IonN-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

NMR Structure (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:183 , GLY A:184 , ARG A:186 , THR A:188 , ASP A:206 , GLU A:209BINDING SITE FOR RESIDUE CA A 273
2AC2SOFTWAREGLU A:164 , ALA A:165 , ASP A:166 , GLU A:197 , GLY A:198 , GLY A:200 , ASP A:202BINDING SITE FOR RESIDUE CA A 274
3AC3SOFTWAREHIS A:176 , ASP A:178 , HIS A:191 , HIS A:204BINDING SITE FOR RESIDUE ZN A 275
4AC4SOFTWAREHIS A:226 , HIS A:230 , HIS A:236 , NGH A:277BINDING SITE FOR RESIDUE ZN A 276
5AC5SOFTWAREGLY A:187 , THR A:188 , LEU A:189 , ALA A:190 , THR A:222 , HIS A:226 , GLU A:227 , HIS A:230 , HIS A:236 , TYR A:245 , PRO A:246 , THR A:247 , TYR A:248 , LYS A:249 , ZN A:276BINDING SITE FOR RESIDUE NGH A 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JSD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JSD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020512D139NMMP20_HUMANPolymorphism17099014AD139N
2UniProtVAR_020513I169LMMP20_HUMANPolymorphism17099008AI169L

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP20_HUMAN223-232  1A:223-232

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002602281ENSE00000930310chr11:102496063-102495925139MMP20_HUMAN1-42420--
1.2ENST000002602282ENSE00000930309chr11:102487790-102487543248MMP20_HUMAN43-125831A:113-12513
1.3ENST000002602283ENSE00000930308chr11:102482634-102482486149MMP20_HUMAN125-175511A:125-17551
1.4ENST000002602284ENSE00000930307chr11:102480761-102480636126MMP20_HUMAN175-217431A:175-21743
1.5ENST000002602285ENSE00000930306chr11:102479829-102479668162MMP20_HUMAN217-271551A:217-27155
1.6ENST000002602286ENSE00000930305chr11:102477407-102477266142MMP20_HUMAN271-318481A:271-2722
1.7ENST000002602287ENSE00000930304chr11:102465488-102465352137MMP20_HUMAN318-364470--
1.8ENST000002602288ENSE00000930303chr11:102464326-102464170157MMP20_HUMAN364-416530--
1.9ENST000002602289ENSE00000930302chr11:102449873-102449770104MMP20_HUMAN416-451360--
1.10ENST0000026022810ENSE00000930301chr11:102448157-102447566592MMP20_HUMAN451-483330--

(-) 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:160
 aligned with MMP20_HUMAN | O60882 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:160
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
          MMP20_HUMAN   113 GEPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWTMGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP 272
               SCOP domains d2jsda_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains 2jsdA00 A:113-272 Collagenase (Catalytic Domain)                                                                                                                 CATH domains
               Pfam domains ---Peptidase_M10-2jsdA01 A:116-271                                                                                                                             - Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh..........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------N-----------------------------L------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2     -------------------------------------------------Exon 1.4  PDB: A:175-217 UniProt: 175-217  -----------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: A:125-175 UniProt: 125-175          -----------------------------------------Exon 1.5  PDB: A:217-271 UniProt: 217-271              - Transcript 1 (2)
                 2jsd A 113 GEPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWTMGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP 272
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272

   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  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (MMP20_HUMAN | O60882)
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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0097186    amelogenesis    The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage.
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0070173    regulation of enamel mineralization    Any process that modulates the frequency, rate or extent of enamel mineralization, the deposition of calcium salts in tooth enamel.
cellular component
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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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