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(-) Description

Title :  COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
 
Authors :  E. Gavuzzo, G. Pochetti, F. Mazza, C. Gallina, B. Gorini, S. D'Alessio, H. Tschesche, P. A. Tucker
Date :  07 Mar 01  (Deposition) - 21 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metalloprotease-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Gavuzzo, G. Pochetti, F. Mazza, C. Gallina, B. Gorini, S. D'Alessio M. Pieper, H. Tschesche, P. A. Tucker
Two Crystal Structures Of Human Neutrophil Collagenase, One Complexed With A Primed- And The Other With An Unprimed-Sid Inhibitor: Implications For Drug Design.
J. Med. Chem. V. 43 3377 2000
PubMed-ID: 10978185  |  Reference-DOI: 10.1021/JM9909589
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUTROPHIL COLLAGENASE
    ChainsA
    EC Number3.4.24.34
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 80-242
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMATRIX METALLOPROTEINASE-8;
MMP-8
 
Molecule 2 - THREE RESIDUE PEPTIDE INHIBITOR
    ChainsB
    EngineeredYES
    Other DetailsTHE THREE RESIDUE PEPTIDE INHIBITOR WAS CHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2PAT1Mod. Amino AcidALPHA-PHOSPHONO-TRYPTOPHAN
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , GLY A:169 , GLY A:171 , ASP A:173 , HOH A:397 , HOH A:402BINDING SITE FOR RESIDUE CA A 996
2AC2SOFTWAREASP A:154 , GLY A:155 , ASN A:157 , ILE A:159 , ASP A:177 , GLU A:180BINDING SITE FOR RESIDUE CA A 997
3AC3SOFTWAREHIS A:147 , ASP A:149 , HIS A:162 , HIS A:175BINDING SITE FOR RESIDUE ZN A 998
4AC4SOFTWAREHIS A:197 , HIS A:201 , HIS A:207 , PAT B:3BINDING SITE FOR RESIDUE ZN A 999
5AC5SOFTWARESER A:151 , ALA A:161 , HIS A:162 , ALA A:163 , PHE A:164 , HIS A:197 , GLU A:198 , HIS A:201 , HIS A:207 , HOH A:329 , HOH A:394 , HOH A:420 , HOH A:555 , ZN A:999 , HOH B:478 , HOH B:500 , HOH B:512BINDING SITE FOR CHAIN B OF THREE RESIDUE PEPTIDE INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I73)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:188 -Tyr A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025038G154EMMP8_HUMANPolymorphism35056226AG134E
2UniProtVAR_025039D193VMMP8_HUMANPolymorphism34428739AD173V
3UniProtVAR_025040N246YMMP8_HUMANPolymorphism35243553AN226Y

  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.MMP8_HUMAN214-223  1A:194-203

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002368262bENSE00002164267chr11:102595685-102595485201MMP8_HUMAN1-34340--
1.6cENST000002368266cENSE00001770190chr11:102593404-102593160245MMP8_HUMAN35-116821A:80-9617
1.7ENST000002368267ENSE00000795297chr11:102592493-102592345149MMP8_HUMAN116-166511A:96-14651
1.8bENST000002368268bENSE00000795296chr11:102592257-102592132126MMP8_HUMAN166-208431A:146-18843
1.9ENST000002368269ENSE00001105479chr11:102589306-102589145162MMP8_HUMAN208-262551A:188-24255
1.10ENST0000023682610ENSE00001105482chr11:102587150-102587033118MMP8_HUMAN262-301401A:242-2421
1.11ENST0000023682611ENSE00001105475chr11:102586168-102586035134MMP8_HUMAN301-346460--
1.12ENST0000023682612ENSE00001105489chr11:102585440-102585287154MMP8_HUMAN346-397520--
1.13ENST0000023682613ENSE00001105495chr11:102584588-102584485104MMP8_HUMAN397-432360--
1.14cENST0000023682614cENSE00001322445chr11:102584188-1025825261663MMP8_HUMAN432-467360--

(-) 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:163
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:163
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
           MMP8_HUMAN   100 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d1i73a_ A: Neutrophil collagenase (MMP-8)                                                                                                                           SCOP domains
               CATH domains 1i73A00 A:80-242 Collagenase (Catalytic Domain)                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------E--------------------------------------V----------------------------------------------------Y---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c        -------------------------------------------------Exon 1.8b  PDB: A:146-188 UniProt: 166-208 -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.7  PDB: A:96-146 UniProt: 116-166           -----------------------------------------Exon 1.9  PDB: A:188-242 UniProt: 208-262               Transcript 1 (2)
                 1i73 A  80 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239   

Chain B from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 1i73 B   1 PLw   3
                              |
                              3-PAT

   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 1I73)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MMP8_HUMAN | P22894)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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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    Asn A:188 - Tyr A:189   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP8_HUMAN | P228941a85 1a86 1bzs 1i76 1jan 1jao 1jap 1jaq 1jh1 1jj9 1kbc 1mmb 1mnc 1zp5 1zs0 1zvx 2oy2 2oy4 3dng 3dpe 3dpf 3tt4 4qkz 5h8x

(-) Related Entries Specified in the PDB File

1bzs CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909
1i76 COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO- ISOQUINOLINE-3-CARBOXYLIC ACID (D-TIC DERIVATIVE) WITH T CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)
1jap COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)