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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE S41 PROTEASE (YP_211611.1) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Oct 09  (Deposition) - 13 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative S41 Protease, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative S41 Protease (Yp_211611. 1) From Bacteroides Fragilis Nctc 9343 At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE S41 PROTEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 24-425
    Gene: BF1979
    Organism Scientific: BACTEROIDES FRAGILIS NCTC 9343
    Organism Taxid: 272559
    Strain: ATCC 25285 / NCTC 9343

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE13Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:119 , HIS A:199 , ARG A:200 , PHE A:404BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWAREASP A:99 , TYR A:100 , THR A:101 , SER A:117 , TYR A:255 , HOH A:444 , HOH A:674BINDING SITE FOR RESIDUE GOL A 2
3AC3SOFTWAREARG A:285 , LYS A:346 , ALA A:383 , THR A:384 , GLY A:385 , HOH A:476 , HOH A:721BINDING SITE FOR RESIDUE GOL A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K50)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:28 -Pro A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K50)

(-) Exons   (0, 0)

(no "Exon" information available for 3K50)

(-) 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:389
 aligned with Q5LDX8_BACFN | Q5LDX8 from UniProtKB/TrEMBL  Length:425

    Alignment length:398
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416        
         Q5LDX8_BACFN    27 RWPEYYPETGRDIWIDSVMRQEYLWYRDMPSPAAPDYFQKPEAFLKKAVASMDNGFSKIDSLLDEPIPSYGFDYTLYKVLDNDTAYNALISYVVPGSPAEEAGLQRGHWIMMMNGDYITKKVESELLQGSTRQLQIGVYKEVVGEDGEVTGGVVPIGETTMPASRSLVDKPVHRFEIIPWNGKKVGYLMYNEFKAGPTTDSQAYNDDLRRAFRDFQTGGVNEFVLDLRYNTGGSLDCAQLLCTMLAPADKMNQLLALLRYSDKRVEANQDLTFNPELIQSGANLNLSTVYVLTTNATRGAAEMVINCLNPYMKVVLIGTKTAGEYVATKPFVHPTDRFILNLVVCNVYNAEEKSDYATGFKPTYEYNEDSYLSTYLPFGNTNETLLNAALKIMSGITD 424
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_S41-3k50A01 A:210-392                                                                                                                                                        -------------------------------- Pfam domains
         Sec.struct. author .......----.hhhhhhhhhhh.hhhhh..........hhhhhhhhhh........eeee..........eeeeeee.......eeeeeeee...hhhhhh......eeeee........hhhhhh....eeeeeeeeeee.-----.eeeeeeeeeeee..........eeeeeeeee..eeeeeeee...........hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh..eeeeee....hhhhheeee.hhhhh.........eeeeee.....hhhhhhhhhhh...eeeeee.......eeeeeee.....eeeeeeeeeee...............ee.hhhhhhhhh.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k50 A  27 RWPEYYP----DIWIDSVmRQEYLWYRDmPSPAAPDYFQKPEAFLKKAVASmDNGFSKIDSLLDEPIPSYGFDYTLYKVLDNDTAYNALISYVVPGSPAEEAGLQRGHWImmmNGDYITKKVESELLQGSTRQLQIGVYKEVV-----VTGGVVPIGETTmPASRSLVDKPVHRFEIIPWNGKKVGYLmYNEFKAGPTTDSQAYNDDLRRAFRDFQTGGVNEFVLDLRYNTGGSLDCAQLLCTmLAPADKmNQLLALLRYSDKRVEANQDLTFNPELIQSGANLNLSTVYVLTTNATRGAAEmVINCLNPYmKVVLIGTKTAGEYVATKPFVHPTDRFILNLVVCNVYNAEEKSDYATGFKPTYEYNEDSYLSTYLPFGNTNETLLNAALKImSGITD 424
                                  |  - |      46        56        66        76 |      86        96       106       116       126       136|||    146       156       166  |    176       186|      196       206       216       226       236       246       256       266   |   276|      286       296       306       316       326  |    336 |     346       356       366       376       386       396       406       416  |     
                                 33   38     45-MSE    55-MSE                 78-MSE                                                    137-MSE                         169   175         187-MSE                     215-MSE                                                270-MSE  |                                                 329-MSE  338-MSE                                                                          419-MSE 
                                                                                                                                         138-MSE                                                                                                                                    277-MSE                                                                                                                                               
                                                                                                                                          139-MSE
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  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 3K50)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K50)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ClpP_crotonase (88)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5LDX8_BACFN | Q5LDX8)
molecular function
    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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    Trp A:28 - Pro A:29   [ RasMol ]  
 

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