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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-16/MT3-MMP: CHARACTERIZATION OF MT-MMP SPECIFIC FEATURES
 
Authors :  R. Lang, M. Braun, N. E. Sounni, A. Noel, F. Frankenne, J. -M. Foidart, W. K. Maskos
Date :  27 Nov 03  (Deposition) - 09 Mar 04  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Mmp-16, Mt3-Mmp, Mt-Mmp, Membrane Type - Matrix Metalloproteinase, Batimastat, Hydroxamate Inhibitor, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Lang, M. Braun, N. E. Sounni, A. Noel, F. Frankenne, J. M. Foidart, W. Bode, K. Maskos
Crystal Structure Of The Catalytic Domain Of Mmp-16/Mt3-Mmp Characterization Of Mt-Mmp Specific Features.
J. Mol. Biol. V. 336 213 2004
PubMed-ID: 14741217  |  Reference-DOI: 10.1016/J.JMB.2003.12.022

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-16
    ChainsA
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7CDMP3
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOMPLEXED WITH BATIMASTAT (BB94)
    SynonymMMP-16;
MT3-MMP;
MEMBRANE-TYPE MATRIX METALLOPROTEINASE 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1BAT1Ligand/Ion4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
2CA2Ligand/IonCALCIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:246 , HIS A:250 , HIS A:256 , BAT A:800BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:193 , ASP A:195 , HIS A:208 , HIS A:221BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWAREASP A:200 , GLY A:201 , GLY A:203 , PHE A:205 , ASP A:223 , GLU A:226BINDING SITE FOR RESIDUE CA A 502
4AC4SOFTWAREASP A:183 , GLY A:215 , ILE A:216 , GLY A:217 , ASP A:219 , HOH A:1076BINDING SITE FOR RESIDUE CA A 504
5AC5SOFTWAREGLY A:194 , GLY A:204 , PHE A:205 , LEU A:206 , ALA A:207 , HIS A:246 , GLU A:247 , HIS A:250 , HIS A:256 , PRO A:260 , PRO A:266 , PHE A:267 , TYR A:268 , ZN A:500 , HOH A:1000 , HOH A:1029BINDING SITE FOR RESIDUE BAT A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RM8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP16_HUMAN243-252  1A:243-252

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002866142aENSE00001399203chr8:89339717-89339304414MMP16_HUMAN1-44440--
1.3ENST000002866143ENSE00001024539chr8:89209535-89209387149MMP16_HUMAN45-94500--
1.4aENST000002866144aENSE00001024546chr8:89198827-89198705123MMP16_HUMAN94-135421A:124-13512
1.5bENST000002866145bENSE00001024542chr8:89180202-89179898305MMP16_HUMAN135-2371031A:135-237103
1.6ENST000002866146ENSE00001793434chr8:89131090-89130929162MMP16_HUMAN237-291551A:237-29155
1.7ENST000002866147ENSE00001088393chr8:89128947-89128736212MMP16_HUMAN291-361711A:291-2922
1.8ENST000002866148ENSE00001088407chr8:89086971-89086833139MMP16_HUMAN362-408470--
1.10ENST0000028661410ENSE00001088408chr8:89068506-89068356151MMP16_HUMAN408-458510--
1.11ENST0000028661411ENSE00001088402chr8:89059012-89058897116MMP16_HUMAN458-497400--
1.12ENST0000028661412ENSE00001260017chr8:89054023-890442379787MMP16_HUMAN497-6071110--

(-) 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:169
 aligned with MMP16_HUMAN | P51512 from UniProtKB/Swiss-Prot  Length:607

    Alignment length:169
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
          MMP16_HUMAN   124 GQKWQHKHITYSIKNVTPKVGDPETRKAIRRAFDVWQNVTPLTFEEVPYSELENGKRDVDITIIFASGFHGDSSPFDGEGGFLAHAYFPGPGIGGDTHFDSDEPWTLGNPNHDGNDLFLVAVHELGHALGLEHSNDPTAIMAPFYQYMETDNFKLPNDDLQGIQKIYGP 292
               SCOP domains d1rm8a_ A: Matrix metalloproteinase-16 (MMP-16)                                                                                                                           SCOP domains
               CATH domains 1rm8A00 A:124-292 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains --Peptidase_M10-1rm8A01 A:126-291                                                                                                                                       - Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee..............eeeeee.................eee..........eeee....ee........eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a   -----------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:237-291 UniProt: 237-291              - Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.5b  PDB: A:135-237 UniProt: 135-237                                                             -----------------------------------------------------1. Transcript 1 (2)
                 1rm8 A 124 GQKWQHKHITYSIKNVTPKVGDPETRKAIRRAFDVWQNVTPLTFEEVPYSELENGKRDVDITIIFASGFHGDSSPFDGEGGFLAHAYFPGPGIGGDTHFDSDEPWTLGNPNHDGNDLFLVAVHELGHALGLEHSNDPTAIMAPFYQYMETDNFKLPNDDLQGIQKIYGP 292
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         

   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  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MMP16_HUMAN | P51512)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0060348    bone development    The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
    GO:0035988    chondrocyte proliferation    The multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
    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:0097094    craniofacial suture morphogenesis    The process in which any suture between cranial and/or facial bones is generated and organized.
    GO:0048701    embryonic cranial skeleton morphogenesis    The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    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

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(-) Related Entries Specified in the PDB File

1bqq CRYSTAL STRUCTURE OF THE MT1-MMP / TIMP-2 COMPLEX
1jk3 CRYSTAL STRUCTURE OF HUMAN MMP-12 (MACROPHAGE ELASTASE) AT TRUE ATOMIC RESOLUTION
1mmb COMPLEX OF BB94 (BATIMASTAT) WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-8 (MMP-8)