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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS METALLOPEPTIDASE (SAPEP/DAPE) IN THE APO-FORM
 
Authors :  T. S. Girish, B. Gopal
Date :  31 Oct 09  (Deposition) - 07 Jul 10  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dipeptidase, Dape, Metallopeptidase, Hydrolase, Metal-Binding, Metalloprotease, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Girish, B. Gopal
Crystal Structure Of Staphylococcus Aureus Metallopeptidase (Sapep) Reveals Large Domain Motions Between The Manganese-Bound And Apo-States
J. Biol. Chem. V. 285 29406 2010
PubMed-ID: 20610394  |  Reference-DOI: 10.1074/JBC.M110.147579

(-) Compounds

Molecule 1 - PUTATIVE DIPEPTIDASE SACOL1801
    Chains: A, B
    EC Number: 3.4.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DIPEPTIDASE PEPV(SACOL1801)
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: METALLOPEPTIDASE, DAPE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3KHX)

(-) Sites  (0, 0)

(no "Site" information available for 3KHX)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:155 -A:178
2B:155 -B:178

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:115 -Asp A:116
2Asp B:115 -Asp B:116
3Asp B:323 -Val B:324
4Asn B:341 -Ala B:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KHX)

(-) 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:422
 aligned with PEPVL_STAAC | Q5HF23 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:470
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469
          PEPVL_STAAC     - -MWKEKVQQYEDQIINDLKGLLAIESVRDDAKASEDAPVGPGPRKALDYMYEIAHRDGFTTHDVDHIAGRIEAGKGNDVLGILCHVDVVPAGDGWDSNPFEPVVTEDAIIARGTLDDKGPTIAAYYAIKILEDMNVDWKKRIHMIIGTDEESDWKCTDRYFKTEEMPTLGFAPDAEFPCIHGEKGITTFDLVQNKLTEDQDEPDYELITFKSGERYNMVPDHAEARVLVKENMTDVIQDFEYFLEQNHLQGDSTVDSGILVLTVEGKAVHGMDPSIGVNAGLYLLKFLASLNLDNNAQAFVAFSNRYLFNSDFGEKMGMKFHTDVMGDVTTNIGVITYDNENAGLFGINLRYPEGFEFEKAMDRFANEIQQYGFEVKLGKVQPPHYVDKNDPFVQKLVTAYRNQTNDMTEPYTIGGGTYARNLDKGVAFGAMFSDSEDLMHQKNEYITKKQLFNATSIYLEAIYSLCVEE 469
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeeee...eeeeeee....eeeeeee.................ee...eee......hhhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhh....eee.............eeeeeeeee...........eeeeeeee.........eeeeeeee..hhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.....------..hhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhh..-------..eeeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhh...-----------------------------------....eeehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khx A   0 SMWKEKVQQYEDQIINDLKGLLAIESVRDDAKASEDAPVGPGPRKALDYMYEIAHRDGFTTHDVDHIAGRIEAGKGNDVLGILCHVDVVPAGDGWDSNPFEPVVTEDAIIARGTLDDKGPTIAAYYAIKILEDMNVDWKKRIHMIIGTDEESDWKCTDRYFKTEEMPTLGFAPDAEFPCIHGEKGITTFDLVQNKLTEDQDEPDYELITFKSGERYNMVPDHAEARVLVKENMTDVIQDFEYFLEQNHLQGDSTVDSGILVLTVEGKAVH------GVNAGLYLLKFLASLNLDNNAQAFVAFSNRYLFNSDFGEKMGMK-------DVTTNIGVITYDNENAGLFGINLRYPEGFEFEKAMDRFANEIQQYGFEVKLGKVQPPHYVDKNDPFVQKLVTAYRNQTN-----------------------------------QKNEYITKKQLFNATSIYLEAIYSLCVEE 469
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      |279       289       299       309       319       329       339       349       359       369       379       389       399     |   -         -         -         - |     449       459       469
                                                                                                                                                                                                                                                                                                       269    276                                        319     327                                                                           405                                 441                            


Chain B from PDB  Type:PROTEIN  Length:425
 aligned with PEPVL_STAAC | Q5HF23 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:469
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       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         
          PEPVL_STAAC     1 MWKEKVQQYEDQIINDLKGLLAIESVRDDAKASEDAPVGPGPRKALDYMYEIAHRDGFTTHDVDHIAGRIEAGKGNDVLGILCHVDVVPAGDGWDSNPFEPVVTEDAIIARGTLDDKGPTIAAYYAIKILEDMNVDWKKRIHMIIGTDEESDWKCTDRYFKTEEMPTLGFAPDAEFPCIHGEKGITTFDLVQNKLTEDQDEPDYELITFKSGERYNMVPDHAEARVLVKENMTDVIQDFEYFLEQNHLQGDSTVDSGILVLTVEGKAVHGMDPSIGVNAGLYLLKFLASLNLDNNAQAFVAFSNRYLFNSDFGEKMGMKFHTDVMGDVTTNIGVITYDNENAGLFGINLRYPEGFEFEKAMDRFANEIQQYGFEVKLGKVQPPHYVDKNDPFVQKLVTAYRNQTNDMTEPYTIGGGTYARNLDKGVAFGAMFSDSEDLMHQKNEYITKKQLFNATSIYLEAIYSLCVEE 469
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------Peptidase_      M20-3khxB01 B:80-464                                                                                                                                                                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------Peptidase_      M20-3khxB02 B:80-464                                                                                                                                                                                                                                                                                                                                                             ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhhh..eeeee...eeeeeee....eeeeeee.....------......ee...eee......hhhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhh....eee.............eeeeeeeee...--......eeeeeeee.........eeeeeeee...hhhhhhhhhhhhhhh..eeeeeee..eeeeeee.......hhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhh.....................eeeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhh.------------------------------------....eeehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khx B   1 MWKEKVQQYEDQIINDLKGLLAIESVRDDAKASEDAPVGPGPRKALDYMYEIAHRDGFTTHDVDHIAGRIEAGKGNDVLGILCHVDVVP------SNPFEPVVTEDAIIARGTLDDKGPTIAAYYAIKILEDMNVDWKKRIHMIIGTDEESDWKCTDRYFKTEEMPTLGFAPDAEFPCIHGEKGITTFDLVQNKL--DQDEPDYELITFKSGERYNMVPDHAEARVLVKENMTDVIQDFEYFLEQNHLQGDSTVDSGILVLTVEGKAVHGMDPSIGVNAGLYLLKFLASLNLDNNAQAFVAFSNRYLFNSDFGEKMGMKFHTDVMGDVTTNIGVITYDNENAGLFGINLRYPEGFEFEKAMDRFANEIQQYGFEVKLGKVQPPHYVDKNDPFVQKLVTAYRNQT------------------------------------QKNEYITKKQLFNATSIYLEAIYSLCVEE 469
                                    10        20        30        40        50        60        70        80        |-     | 100       110       120       130       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   |     -         -         -         -|      450       460         
                                                                                                                   89     96                                                                                                195  |                                                                                                                                                                                                           404                                  441                            
                                                                                                                                                                                                                               198
   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 3KHX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PEPVL_STAAC | Q5HF23)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  Cis Peptide Bonds
    Asn B:341 - Ala B:342   [ RasMol ]  
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  3.4.13.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PEPVL_STAAC | Q5HF23: 3khz 3ki9

(-) Related Entries Specified in the PDB File

3khz CRYSTAL STRUCTURE OF R350A MUTANT OF STAPHYLOCOCCUS AUREUS METALLOPEPTIDASE (SAPEP/DAPE) IN THE APO-FORM
3ki9 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS METALLOPEPTIDASE (SAPEP/DAPE) IN THE MN2+ BOUND FORM