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(-) Description

Title :  SOLUTION STRUCTURE OF MATRIX METALLOPROTEINASE 12 (MMP12) IN THE PRESENCE OF N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID (NNGH)
 
Authors :  I. Bertini, V. Calderone, M. Cosenza, M. Fragai, Y. M. Lee, C. Luchinat, S. Mangani, B. Terni, P. Turano, Structural Proteomics In Europe (Spine)
Date :  22 Dec 04  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Macrophage Metalloelastase, Mmp-12, Solution Structure, Nngh, Zinc, Calcium, Structural Proteomics In Europe, Spine, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Bertini, V. Calderone, M. Cosenza, M. Fragai, Y. M. Lee, C. Luchinat, S. Mangani, B. Terni, P. Turano
Conformational Variability Of Matrix Metalloproteinases: Beyond A Single 3D Structure.
Proc. Natl. Acad. Sci. Usa V. 102 5334 2005
PubMed-ID: 15809432  |  Reference-DOI: 10.1073/PNAS.0407106102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    ChainsA
    EC Number3.4.24.65
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneMMP12, HME
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE ELASTASE, ME

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

NMR Structure (3, 6)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2NGH1Ligand/IonN-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

NMR Structure (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , NGH A:269BINDING SITE FOR RESIDUE ZN A 264
2AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A 265
3AC3SOFTWARETHR A:122 , ASP A:124 , GLU A:199 , GLU A:201BINDING SITE FOR RESIDUE CA A 266
4AC4SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A 267
5AC5SOFTWAREGLY A:190 , ILE A:191 , GLY A:192 , ASP A:194BINDING SITE FOR RESIDUE CA A 268
6AC6SOFTWARELEU A:181 , ALA A:182 , LEU A:214 , THR A:215 , HIS A:218 , GLU A:219 , PRO A:238 , THR A:239 , TYR A:240 , ZN A:264BINDING SITE FOR RESIDUE NGH A 269

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YCM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YCM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YCM)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP12_HUMAN215-224  1A:215-224

(-) Exons   (0, 0)

(no "Exon" information available for 1YCM)

(-) 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:159
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:159
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
          MMP12_HUMAN   105 GGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
               SCOP domains d1ycma_ A: Macrophage elastase (MMP-12)                                                                                                                         SCOP domains
               CATH domains 1ycmA00 A:105-263 Collagenase (Catalytic Domain)                                                                                                                CATH domains
               Pfam domains ---Peptidase_M10-1ycmA01 A:108-263                                                                                                                              Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ycm A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         

   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  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (MMP12_HUMAN | P39900)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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: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:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0060054    positive regulation of epithelial cell proliferation involved in wound healing    Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
    GO:0035313    wound healing, spreading of epidermal cells    The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
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: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
        MMP12_HUMAN | P399001jiz 1jk3 1os2 1os9 1rmz 1ros 1utt 1utz 1y93 1z3j 2hu6 2jxy 2k2g 2k9c 2krj 2mlr 2mls 2n8r 2oxu 2oxw 2oxz 2poj 2w0d 2wo8 2wo9 2woa 2z2d 3ba0 3ehx 3ehy 3f15 3f16 3f17 3f18 3f19 3f1a 3lik 3lil 3lir 3ljg 3lk8 3lka 3n2u 3n2v 3nx7 3rts 3rtt 3ts4 3tsk 3uvc 4efs 4gql 4gr0 4gr3 4gr8 4guy 4h30 4h49 4h76 4h84 4i03 4ijo 5cxa 5czm 5d2b 5d3c 5i0l 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

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