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(-) Description

Title :  INHIBITOR-FREE CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  R. Powers, F. J. Moy
Date :  06 Nov 97  (Deposition) - 25 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Matrix Metalloproteinase, Hydrolase, Metalloprotease, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. J. Moy, P. K. Chanda, S. Cosmi, M. R. Pisano, C. Urbano, J. Wilhelm, R. Powers
High-Resolution Solution Structure Of The Inhibitor-Free Catalytic Fragment Of Human Fibroblast Collagenase Determined By Multidimensional Nmr.
Biochemistry V. 37 1495 1998
PubMed-ID: 9484219  |  Reference-DOI: 10.1021/BI972181W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGENASE
    Cell LineBL21
    ChainsA
    EC Number3.4.24.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNOT-3A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPET-21A(+)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMMP-1, FIBROBLAST COLLAGENASE

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

NMR Structure (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

NMR Structure (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:118 , HIS A:122 , HIS A:128BINDING SITE FOR RESIDUE ZN A 170
2AC2SOFTWAREHIS A:68 , ASP A:70 , HIS A:83 , HIS A:96BINDING SITE FOR RESIDUE ZN A 171
3AC3SOFTWAREGLY A:76 , GLY A:78 , ASN A:80 , ASP A:98 , GLU A:101BINDING SITE FOR RESIDUE CA A 172
4CABUNKNOWNGLY A:76 , GLY A:78 , ASN A:80CA BINDING SITE.
5ZNAUNKNOWNHIS A:118 , HIS A:122 , HIS A:128ZN BINDING SITE.
6ZNBUNKNOWNHIS A:68 , HIS A:83 , HIS A:96ZN BINDING SITE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021024I191VMMP1_HUMANPolymorphism17879973AI91V
2UniProtVAR_011970D252GMMP1_HUMANPolymorphism513964AD152G
3UniProtVAR_054005R262SMMP1_HUMANPolymorphism12282811AR162S

  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.MMP1_HUMAN215-224  1A:115-124

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003152741ENSE00001234609chr11:102668891-102668719173MMP1_HUMAN1-35350--
1.2ENST000003152742ENSE00000993211chr11:102668231-102667987245MMP1_HUMAN36-117821A:7-1711
1.3ENST000003152743ENSE00000993213chr11:102667893-102667745149MMP1_HUMAN117-167511A:17-6751
1.4ENST000003152744ENSE00001105440chr11:102667520-102667395126MMP1_HUMAN167-209431A:67-10943
1.5ENST000003152745ENSE00000993197chr11:102666338-102666183156MMP1_HUMAN209-261531A:109-16153
1.6ENST000003152746ENSE00000993183chr11:102666022-102665905118MMP1_HUMAN261-300401A:161-1633
1.7ENST000003152747ENSE00000993195chr11:102663469-102663336134MMP1_HUMAN300-345460--
1.8ENST000003152748ENSE00000993199chr11:102662226-102662064163MMP1_HUMAN345-399550--
1.9ENST000003152749ENSE00000993204chr11:102661537-102661434104MMP1_HUMAN399-434360--
1.10ENST0000031527410ENSE00001234621chr11:102661252-102660651602MMP1_HUMAN434-469360--

(-) 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:157
 aligned with MMP1_HUMAN | P03956 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:157
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       
           MMP1_HUMAN   107 PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRS 263
               SCOP domains d2ayka_ A: Fibroblast collagenase (MMP-1)                                                                                                                     SCOP domains
               CATH domains 2aykA00 A:7-163 Collagenase (Catalytic Domain)                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee........hhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhh..........................hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------V------------------------------------------------------------G---------S- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   -------------------------------------------------Exon 1.4  PDB: A:67-109 UniProt: 167-209   ---------------------------------------------------1.6 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.3  PDB: A:17-67 UniProt: 117-167            -----------------------------------------Exon 1.5  PDB: A:109-161 UniProt: 209-261            -- Transcript 1 (2)
                 2ayk A   7 PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRS 163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       

   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  (0, 0)

(no "Pfam Domain" information available for 2AYK)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (MMP1_HUMAN | P03956)
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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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
        MMP1_HUMAN | P039561ayk 1cge 1cgf 1cgl 1hfc 1su3 2clt 2j0t 2tcl 3ayk 3shi 4auo 4ayk 966c

(-) Related Entries Specified in the PDB File

1ayk