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(-) Description

Title :  MATRILYSIN COMPLEXED WITH HYDROXAMATE INHIBITOR
 
Authors :  M. F. Browner, W. W. Smith, A. L. Castelhano
Date :  22 Mar 95  (Deposition) - 03 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. F. Browner, W. W. Smith, A. L. Castelhano
Matrilysin-Inhibitor Complexes: Common Themes Among Metalloproteases.
Biochemistry V. 34 6602 1995
PubMed-ID: 7756291  |  Reference-DOI: 10.1021/BI00020A004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATRILYSIN
    ChainsA
    EC Number3.4.24.23
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    OrganOVARY
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMMP-9, PUMP-1, MATRIN

 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
1CA2Ligand/IonCALCIUM ION
2RRS1Ligand/IonN4-HYDROXY-2-ISOBUTYL-N1-(9-OXO-1,8-DIAZA-TRICYCLO[10.6.1.013,18]NONADECA-12(19),13,15,17-TETRAEN-10-YL)-SUCCINAMIDE
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , RRS A:269BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , THR A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A 3
4AC4SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:313 , HOH A:317BINDING SITE FOR RESIDUE CA A 4
5AC5SOFTWAREZN A:1 , VAL A:153 , ASN A:179 , THR A:180 , LEU A:181 , ALA A:182 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PRO A:232 , PRO A:238 , THR A:239 , TYR A:240 , HOH A:328 , HOH A:356BINDING SITE FOR RESIDUE RRS A 269

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021027G137DMMP7_HUMANPolymorphism17884789AG142D
2UniProtVAR_021028P241LMMP7_HUMANPolymorphism17886506AP245L

  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.MMP7_HUMAN211-220  1A:215-224

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002602271aENSE00002145134chr11:102401484-102401324161MMP7_HUMAN1-36360--
1.2ENST000002602272ENSE00000930299chr11:102398714-102398488227MMP7_HUMAN37-112761A:100-11718
1.3aENST000002602273aENSE00000930298chr11:102398403-102398255149MMP7_HUMAN112-162511A:117-16751
1.4aENST000002602274aENSE00000930297chr11:102395795-102395667129MMP7_HUMAN162-205441A:167-20944
1.5ENST000002602275ENSE00000930296chr11:102394132-102393971162MMP7_HUMAN205-259551A:209-26355
1.6ENST000002602276ENSE00001252223chr11:102391535-102391239297MMP7_HUMAN259-26791A:263-2642

(-) 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:166
 aligned with MMP7_HUMAN | P09237 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:166
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          MMP7_HUMAN     95 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  260
               SCOP domains d1mmqa_ A: Matrilysin (MMP-7)                                                                                                                                          SCOP domains
               CATH domains 1mmqA00 A:100-264 Collagenase (Catalytic Domain)                                                                                                                       CATH domains
               Pfam domains --------Peptidase_M10-1mmqA01 A:108-263                                                                                                                              - Pfam domains
         Sec.struct. author ....hhh......eeeeee........hhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee..............hhhhhhhhhhhhh...........................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------D-------------------------------------------------------------------------------------------------------L------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4a  PDB: A:167-209 UniProt: 162-205  -----------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3a  PDB: A:117-167 UniProt: 112-162         ------------------------------------------Exon 1.5  PDB: A:209-263 UniProt: 205-259              - Transcript 1 (2)
                1mmq A  100 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  264
                                   109       119       129       139       149       159       169       179       189       199      208B       218       228       238       248       258      
                                                                                                                                      208B                                                        

   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  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MMP7_HUMAN | P09237)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    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:0044849    estrous cycle    A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0031667    response to nutrient levels    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 stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        MMP7_HUMAN | P092371mmp 1mmr 2ddy 2mze 2mzh 2mzi 2y6c 2y6d

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