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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUBTILISIN-LIKE PROTEASE
 
Authors :  C. J. Porter, W. Wong, J. C. Whisstock, J. I. Rood, R. M. Kennan
Date :  05 Feb 10  (Deposition) - 08 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Protease, Subtilase, Virulence Factor, Hydrolase, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Kennan, W. Wong, O. P. Dhungyel, X. Han, D. Wong, D. Parker, C. J. Rosado, R. H. P. Law, S. Mcgowan, S. B. Reeve, V. Levina, G. A. Powers, R. N. Pike, S. P. Bottomley, A. I. Smith, I. Marsh, R. J. Whittington, J. C. Whisstock, C. J. Porter, J. I. Rood
The Subtilisin-Like Protease Aprv2 Is Required For Virulenc And Uses A Novel Disulphide-Tethered Exosite To Bind Substrates
Plos Pathog. V. 6 E1001 2010
PubMed-ID: 21124876  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001210

(-) Compounds

Molecule 1 - ACIDIC EXTRACELLULAR SUBTILISIN-LIKE PROTEASE APRV2
    Chains: A
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ROSETTA-GAMI(DE3)LYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 131-469
    Gene: APRV2, DNO_1167
    Mutation: YES
    Organism Scientific: DICHELOBACTER NODOSUS
    Organism Taxid: 246195
    Strain: VCS1703A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:5 , ASP A:49 , VAL A:116 , ASN A:119 , ILE A:121 , VAL A:123BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREASP A:59 , ASP A:69 , ASP A:74 , ASP A:76 , HOH A:405BINDING SITE FOR RESIDUE CA A 341
3AC3SOFTWAREASP A:69 , ASP A:71 , GLY A:72 , ASP A:74 , HOH A:374BINDING SITE FOR RESIDUE CA A 342

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:183 -A:220

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:92 -Pro A:93
2Trp A:216 -Pro A:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LPD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LPD)

(-) Exons   (0, 0)

(no "Exon" information available for 3LPD)

(-) 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:339
 aligned with A5EXI3_DICNV | A5EXI3 from UniProtKB/TrEMBL  Length:601

    Alignment length:339
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460         
         A5EXI3_DICNV   131 APNDQHYREQWHYFDRYGVKADKVWDMGFTGQNVVVAVVDTGILHHRDLNANVLPGYDFISNSQISLDGDGRDADPFDEGDWFDNWACGGYPDPRKERSDSSWHGSHVAGTIAAVTNNRIGVAGVAYGAKVVPVRALGRCGGYDSDISDGLYWAAGGRIAGIPENRNPAKVINMSLGSDGQCSYNAQTMIDRATRLGALVVVAAGNENQNASNTWPTSCNNVLSVGATTSRGIRASFSNYGVDVDLAAPGQDILSTVDSGTRRPVSDAYSFMAGTSMATPHVSGVAALVISAANSVNKNLTPAELKDVLVSTTSPFNGRLDRALGSGIVDAEAAVNSVL 469
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------Peptidase_S8-3lpdA01 A:36-337                                                                                                                                                                                                                                                                                 --- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhh........eeeeee........hhhhh...ee...hhhhhh.........................hhhhh.....hhhhhhhhhhhh...............eeeeee.......hhhhhhhhhhhhh...............eeee...ee...hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.................eeee...eeeeee........eeeeee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.................hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lpd A   2 APNDQHYREQWHYFDRYGVKADKVWDMGFTGQNVVVAVVDTGILHHRDLNANVLPGYDFISNSQISLDGDGRDADPFDEGDWFDNWACGGYPDPRKERSDSSWHGSHVAGTIAAVTNNRIGVAGVAYGAKVVPVRALGRSGGYDSDISDGLYWAAGGRIAGIPENRNPAKVINMSLGSDGQCSYNAQTMIDRATRLGALVVVAAGNENQNASNTWPTSCNNVLSVGATTSRGIRASFSNYGVDVDLAAPGQDILSTVDSGTRRPVSDAYSFMAGTSMATPHVSGVAALVISAANSVNKNLTPAELKDVLVSTTSPFNGRLDRALGSGIVDAEAAVNSVL 340
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
   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 3LPD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LPD)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A5EXI3_DICNV | A5EXI3)
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: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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of 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).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

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        A5EXI3_DICNV | A5EXI3: 3lpa

(-) Related Entries Specified in the PDB File

3lpa 3lpc