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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MMP-12 IN COMPLEX WITH ACETOHYDROXAMIC ACID AND A BICYCLIC INHIBITOR
 
Authors :  C. Mannino, M. Nievo, F. Machetti, A. Papakyriakou, V. Calderone, M. Fragai, A. Guarna
Date :  26 Jul 06  (Deposition) - 19 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Mmp-12, Matrix Metalloproteinase, Macrophage Metalloelastase, Inhibitor, Hydroxamic Acid, Drug Design, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Mannino, M. Nievo, F. Machetti, A. Papakyriakou, V. Calderone, M. Fragai, A. Guarna
Synthesis Of Bicyclic Molecular Scaffolds (Btaa): An Investigation Towards New Selective Mmp-12 Inhibitors.
Bioorg. Med. Chem. V. 14 7392 2006
PubMed-ID: 16899369  |  Reference-DOI: 10.1016/J.BMC.2006.07.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    ChainsA
    EC Number3.4.24.65
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN (RESIDUES 106-263)
    GeneMMP12, HME
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE ELASTASE, ME

 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
137A1Ligand/Ion(1S,5S,7R)-N~7~-(BIPHENYL-4-YLMETHYL)-N~3~-HYDROXY-6,8-DIOXA-3-AZABICYCLO[3.2.1]OCTANE-3,7-DICARBOXAMIDE
2CA3Ligand/IonCALCIUM ION
3HAE1Ligand/IonACETOHYDROXAMIC ACID
4ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , HAE A:269 , HOH A:655BINDING SITE FOR RESIDUE ZN A 264
2AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A 265
3AC3SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:405 , HOH A:470BINDING SITE FOR RESIDUE CA A 266
4AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:410 , HOH A:428BINDING SITE FOR RESIDUE CA A 267
5AC5SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A 268
6AC6SOFTWAREGLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:218 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , LYS A:241 , HOH A:446 , HOH A:460 , HOH A:468 , HOH A:474 , HOH A:535 , HOH A:656BINDING SITE FOR RESIDUE 37A A 400
7AC7SOFTWAREALA A:182 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , ZN A:264 , HOH A:655BINDING SITE FOR RESIDUE HAE A 269

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HU6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (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 2HU6)

(-) 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:158
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:158
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
          MMP12_HUMAN   106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
               SCOP domains d2hu6a_ A: Macrophage elastase (MMP-12)                                                                                                                        SCOP domains
               CATH domains 2hu6A00 A:106-263 Collagenase (Catalytic Domain)                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hu6 A 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        

   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 2HU6)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(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 1ycm 1z3j 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

1rmz CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 COMPLEXED WITH THE INHIBITOR NNGH AT 1.3 A RESOLUTION.
1y93 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 COMPLEXED WITH ACETOHYDROXAMIC ACID AT ATOMIC RESOLUTION.