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(-) Description

Title :  STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN
 
Authors :  N. Cerda-Costa, T. Guevara, A. Y. Karim, M. Ksiazek, K. -A. Nguyen, J. L. J. Potempa, F. X. Gomis-Ruth
Date :  24 Sep 10  (Deposition) - 03 Nov 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase, Bacterial Mmp, Virulence Factor, Metalloprotease, Zinc- Dependent, Peptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Cerda-Costa, T. Guevara, A. Y. Karim, M. Ksiazek, K. A. Nguyen, J. L. Arolas, J. Potempa, F. X. Gomis-Ruth
The Structure Of The Catalytic Domain Of Tannerella Forsythia Karilysin Reveals It Is A Bacterial Xenologue Of Animal Matrix Metalloproteinases.
Mol. Microbiol. V. 79 119 2011
PubMed-ID: 21166898  |  Reference-DOI: 10.1111/J.1365-2958.2010.07434.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KARILYSIN PROTEASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 35-200
    Organism ScientificTANNERELLA FORSYTHIA
    Organism Taxid28112
    SynonymKARILYSIN CATALYTIC DOMAIN KLY18
 
Molecule 2 - PEPTIDE ALA-PHE-THR-SER
    ChainsC, D
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:102 , ASP A:104 , HIS A:117 , HIS A:133BINDING SITE FOR RESIDUE ZN A 998
2AC2SOFTWAREHIS A:155 , HIS A:159 , HIS A:165 , ALA C:201BINDING SITE FOR RESIDUE ZN A 999
3AC3SOFTWAREHIS B:102 , ASP B:104 , HIS B:117 , HIS B:133BINDING SITE FOR RESIDUE ZN B 998
4AC4SOFTWAREHIS B:155 , HIS B:159 , HIS B:165 , ALA D:201BINDING SITE FOR RESIDUE ZN B 999
5AC5SOFTWARETYR B:106 , ALA B:118 , PHE B:119 , GLN B:183BINDING SITE FOR RESIDUE TRS B1305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XS3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:122 -Pro A:123
2Pro B:122 -Pro B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XS3)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.KLY_TANFA152-161
 
  2A:152-161
B:152-161
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.KLY_TANFA152-161
 
  1A:152-161
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.KLY_TANFA152-161
 
  1-
B:152-161

(-) Exons   (0, 0)

(no "Exon" information available for 2XS3)

(-) Sequences/Alignments

Asymmetric 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 KLY_TANFA | D0EM77 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:166
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      
            KLY_TANFA    35 YVLQGSKWNKTTLKYYIYNSSSHLTTTERENAIRSAFALWSDKSTLSFIQVYNPNQADIKIKWEKGNHGDGYPFDGNTGILAHAFYPPPAGGNYAGHLHFDGDENWSINGSGIDLITVAAHEIGHLLGIEHSNVSSALMYPYYTGIKRQLDNDDCLAVWDLYGYPF 200
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee..hhhhh.eeeeee.................eee......hhhhh.eeeee....ee.....eehhhhhhhhhhhhhh......................hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xs3 A  35 YVLQGSKWNKTTLKYYIYNSSSHLTTTERENAIRSAFALWSDKSTLSFIQVYNPNQADIKIKWEKGNHGDGYPFDGNTGILAHAFYPPPAGGNYAGHLHFDDDENWSINGSGIDLITVAAHEIGHLLGIEHSNVSSALMYPYYTGIKRQLDNDDCLAVWDLYGYPF 200
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with KLY_TANFA | D0EM77 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:166
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      
            KLY_TANFA    35 YVLQGSKWNKTTLKYYIYNSSSHLTTTERENAIRSAFALWSDKSTLSFIQVYNPNQADIKIKWEKGNHGDGYPFDGNTGILAHAFYPPPAGGNYAGHLHFDGDENWSINGSGIDLITVAAHEIGHLLGIEHSNVSSALMYPYYTGIKRQLDNDDCLAVWDLYGYPF 200
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee..hhhhh.eeeeee.................eee......hhhhh.eeeee....ee.....eehhhhhhhhhhhhhh......................hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xs3 B  35 YVLQGSKWNKTTLKYYIYNSSSHLTTTERENAIRSAFALWSDKSTLSFIQVYNPNQADIKIKWEKGNHGDGYPFDGNTGILAHAFYPPPAGGNYAGHLHFDDDENWSINGSGIDLITVAAHEIGHLLGIEHSNVSSALMYPYYTGIKRQLDNDDCLAVWDLYGYPF 200
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      

Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 2xs3 C 201 AFTS 204

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               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
                 2xs3 D 201 AFTS 204

   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  (0, 0)

(no "SCOP Domain" information available for 2XS3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XS3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XS3)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KLY_TANFA | D0EM77)
molecular function
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KLY_TANFA | D0EM772xs4 4in9 4r3v

(-) Related Entries Specified in the PDB File

2xs4 STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN IN COMPLEX WITH MAGNESIUM