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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-702,842
 
Authors :  J. W. Becker
Date :  03 Aug 95  (Deposition) - 17 Dec 96  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metalloprotease, Fibroblast, Collagen Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Becker, A. I. Marcy, L. L. Rokosz, M. G. Axel, J. J. Burbaum, P. M. Fitzgerald, P. M. Cameron, C. K. Esser, W. K. Hagmann, J. D. Hermes J. P. Springer
Stromelysin-1: Three-Dimensional Structure Of The Inhibited Catalytic Domain And Of The C-Truncated Proenzyme.
Protein Sci. V. 4 1966 1995
PubMed-ID: 8535233
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STROMELYSIN-1
    CellFIBROBLAST
    ChainsA
    EC Number3.4.24.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN RESIDUES 83 - 255
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMATRIX METALLOPROTEINASE-3, PROTEOGLYCANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2INH1Ligand/IonN-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L-ARGININE-N-PHENYLAMIDE
3ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:201 , HIS A:205 , HIS A:211 , INH A:256BINDING SITE FOR RESIDUE ZN A 257
02AC2SOFTWAREHIS A:151 , ASP A:153 , HIS A:166 , HIS A:179BINDING SITE FOR RESIDUE ZN A 258
03AC3SOFTWAREASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184BINDING SITE FOR RESIDUE CA A 259
04AC4SOFTWAREASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:306 , HOH A:312BINDING SITE FOR RESIDUE CA A 260
05AC5SOFTWAREASP A:107 , ASP A:182 , GLU A:184BINDING SITE FOR RESIDUE CA A 261
06AC6SOFTWAREGLY A:152 , ASP A:153 , PHE A:154 , ASN A:162 , LEU A:164 , ALA A:165 , LEU A:197 , VAL A:198 , HIS A:201 , GLU A:202 , HIS A:205 , HIS A:211 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , ZN A:257 , HOH A:301 , HOH A:502 , HOH A:504 , HOH A:519BINDING SITE FOR RESIDUE INH A 256
07CA1UNKNOWNASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184CA1 ARE THE LIGANDS OF THE CALCIUM ION CA 259
08CA2UNKNOWNASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:306 , HOH A:312CA2 ARE THE LIGANDS OF THE CALCIUM ION CA 260
09CA3UNKNOWNASP A:107 , ASP A:182 , GLU A:184CA3 ARE THE LIGANDS OF THE CALCIUM ION CA 261
10INHUNKNOWNASN A:162 , VAL A:163 , LEU A:164 , ALA A:165 , LEU A:197 , VAL A:198 , HIS A:201 , GLU A:202 , HIS A:205 , HIS A:211 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , ZN A:257 , HOH A:301 , HOH A:502SITE INH IS THE BINDING SITE FOR THE N-CARBOXY- ALKYL INHIBITOR L-702,842, DENOTED INH 256.
11ZN1UNKNOWNHIS A:201 , HIS A:205 , HIS A:211 , INH A:256ZN1 ARE THE LIGANDS OF THE CATALYTIC (ZN 257) ZINC ION.
12ZN2UNKNOWNHIS A:151 , ASP A:153 , HIS A:166 , HIS A:179ZN2 ARE THE LIGANDS OF THE STRUCTURAL (ZN 258) ZINC ION.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224  1A:198-207

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002998551aENSE00002171374chr11:102714534-102714173362MMP3_HUMAN1-35350--
1.2ENST000002998552ENSE00001105428chr11:102713647-102713403245MMP3_HUMAN36-117821A:83-10018
1.3ENST000002998553ENSE00001642002chr11:102713310-102713162149MMP3_HUMAN117-167511A:100-15051
1.4bENST000002998554bENSE00001105420chr11:102713010-102712885126MMP3_HUMAN167-209431A:150-19243
1.5ENST000002998555ENSE00001657829chr11:102711324-102711160165MMP3_HUMAN209-264561A:192-24756
1.6ENST000002998556ENSE00001105427chr11:102710983-102710839145MMP3_HUMAN264-312491A:247-2504
1.7ENST000002998557ENSE00001105439chr11:102709974-102709841134MMP3_HUMAN312-357460--
1.8ENST000002998558ENSE00001801971chr11:102709441-102709282160MMP3_HUMAN357-410540--
1.9ENST000002998559ENSE00001105448chr11:102708132-102708029104MMP3_HUMAN410-445360--
1.11ENST0000029985511ENSE00001292630chr11:102706957-102706532426MMP3_HUMAN445-477330--

(-) 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:168
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:168
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 267
               SCOP domains d1slna_ A: Stromelysin-1 (MMP-3)                                                                                                                                         SCOP domains
               CATH domains 1slnA00 A:83-250 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains --------Peptidase_M10-1slnA01 A:91-247                                                                                                                               --- Pfam domains
         Sec.struct. author ............eeeeeee........hhhhhhhhhhhhhhhh.....eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhh.............................hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4b  PDB: A:150-192 UniProt: 167-209 ------------------------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: A:100-150 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: A:192-247 UniProt: 209-264               --- Transcript 1 (2)
                 1sln A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        

   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  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MMP3_HUMAN | P08254)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0071732    cellular response to nitric oxide    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 nitric oxide 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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0010727    negative regulation of hydrogen peroxide metabolic process    Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.
    GO:1903209    positive regulation of oxidative stress-induced cell death    Any process that activates or increases the frequency, rate or extent of oxidative stress-induced cell death.
    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.
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: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)

UniProtKB/Swiss-Prot
        MMP3_HUMAN | P082541b3d 1b8y 1biw 1bm6 1bqo 1c3i 1c8t 1caq 1ciz 1cqr 1d5j 1d7x 1d8f 1d8m 1g05 1g49 1g4k 1hfs 1hy7 1m1w 1oo9 1qia 1qic 1slm 1uea 1ums 1umt 1usn 2d1o 2jnp 2jt5 2jt6 2srt 2usn 3ohl 3oho 3usn 4dpe 4g9l 4ja1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SLN)