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(-) Description

Title :  CRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGENASE COMPLEXED TO ITSELF
 
Authors :  B. Lovejoy, A. M. Hassell, M. A. Luther, D. Weigl, S. R. Jordan
Date :  03 Feb 94  (Deposition) - 31 Mar 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Metalloprotease) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Lovejoy, A. M. Hassell, M. A. Luther, D. Weigl, S. R. Jordan
Crystal Structures Of Recombinant 19-Kda Human Fibroblast Collagenase Complexed To Itself.
Biochemistry V. 33 8207 1994
PubMed-ID: 8031754  |  Reference-DOI: 10.1021/BI00193A006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBLAST COLLAGENASE
    ChainsA
    EC Number3.4.24.7
    EngineeredYES
    GeneCDNA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:102 , HIS A:218 , HIS A:222 , HIS A:228BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ASN A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A 303
4AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:570 , HOH A:600BINDING SITE FOR RESIDUE CA A 304
5AC5SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:544 , HOH A:566BINDING SITE FOR RESIDUE CA A 305
6CATUNKNOWNZN A:301 , GLY A:179 , ASN A:180 , LEU A:181 , ALA A:182 , GLU A:219 , PRO A:238 , TYR A:240 , ARG A:214 , VAL A:215NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021024I191VMMP1_HUMANPolymorphism17879973AI191V
2UniProtVAR_011970D252GMMP1_HUMANPolymorphism513964AD252G
3UniProtVAR_054005R262SMMP1_HUMANPolymorphism12282811AR262S

  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.MMP1_HUMAN215-224  1A:215-224

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003152741ENSE00001234609chr11:102668891-102668719173MMP1_HUMAN1-35350--
1.2ENST000003152742ENSE00000993211chr11:102668231-102667987245MMP1_HUMAN36-117821A:102-11716
1.3ENST000003152743ENSE00000993213chr11:102667893-102667745149MMP1_HUMAN117-167511A:117-16751
1.4ENST000003152744ENSE00001105440chr11:102667520-102667395126MMP1_HUMAN167-209431A:167-20943
1.5ENST000003152745ENSE00000993197chr11:102666338-102666183156MMP1_HUMAN209-261531A:209-26153
1.6ENST000003152746ENSE00000993183chr11:102666022-102665905118MMP1_HUMAN261-300401A:261-2633
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

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:162
 aligned with MMP1_HUMAN | P03956 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:162
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
           MMP1_HUMAN   102 LTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRS 263
               SCOP domains d1cgea_ A: Fibroblast collagenase (MMP-1)                                                                                                                          SCOP domains
               CATH domains 1cgeA00 A:102-263 Collagenase (Catalytic Domain)                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee..........hhhhhhhhhhhhhhhh..eeeeeee....eeeeeee.................eeee........eeeeee............hhhhhhhhhhhh..........................hhhhhhhhhhh... 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:167-209 UniProt: 167-209  ---------------------------------------------------1.6 Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3  PDB: A:117-167 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: A:209-261 UniProt: 209-261            -- Transcript 1 (2)
                 1cge A 102 LTEGNPRWEQTHLRYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRS 263
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  

   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 1CGE)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(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 1cgf 1cgl 1hfc 1su3 2ayk 2clt 2j0t 2tcl 3ayk 3shi 4auo 4ayk 966c

(-) Related Entries Specified in the PDB File

1cgf 1cgl