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(-) Description

Title :  CRYSTAL STRUCTURE OF SCYTALIDO-GLUTAMIC PEPTIDASE WITH A PEPTIDE BASED TRANSITION STATE ANALOG
 
Authors :  B. Pillai, M. M. Cherney, K. Hiraga, K. Takada, K. Oda, M. N. James
Date :  21 Sep 06  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme-Transition State Analog Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pillai, M. M. Cherney, K. Hiraga, K. Takada, K. Oda, M. N. James
Crystal Structure Of Scytalidoglutamic Peptidase With Its First Potent Inhibitor Provides Insights Into Substrate Specificity And Catalysis.
J. Mol. Biol. V. 365 343 2007
PubMed-ID: 17069854  |  Reference-DOI: 10.1016/J.JMB.2006.09.058

(-) Compounds

Molecule 1 - SCYTALIDOPEPSIN B
    Chains: A
    EC Number: 3.4.23.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SCYTALIDIUM LIGNICOLA
    Organism Taxid: 5539
    Synonym: ACID PROTEASE B, SLB
 
Molecule 2 - OCTAPEPTIDE
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ACY1Ligand/IonACETIC ACID
3NH21Mod. Amino AcidAMINO GROUP
4TA21Mod. Amino Acid(2R,3S)-3-AMINO-3-PHENYLPROPANE-1,2-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:74 , LYS A:116 , SER A:119 , GLU A:121BINDING SITE FOR RESIDUE ACY A 437
2AC2SOFTWARETHR A:1 , VAL A:2 , ASN A:5 , TRP A:6 , THR A:37 , GLY A:44 , ASP A:45 , GLN A:53 , ASP A:57 , TYR A:59 , TRP A:67 , GLU A:69 , TYR A:71 , GLU A:136 , PHE A:138 , GLU A:139 , GLU A:140 , CYS A:141 , ASN A:142 , SER A:143 , THR A:182 , HOH B:338 , HOH B:401 , HOH B:435 , HOH B:436BINDING SITE FOR CHAIN B OF OCTAPEPTIDE

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:47 -A:127
2A:141 -A:148
3A:194 -A:203

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:71 -Pro A:72
2Ser A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IFR)

(-) Exons   (0, 0)

(no "Exon" information available for 2IFR)

(-) 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:204
 aligned with PRTB_SCYLI | P15369 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:206
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
           PRTB_SCYLI    55 TVESNWGGAILIGSDFDTVSATANVPSASGGSSAAGTAWVGIDGDTCQTAILQTGFDWYGDGTYDAWYEWYPEVSDDFSGITISEGDSIQMSVTATSDTSGSATLENLTTGQKVSKSFSNESSGSLCRTNAEFIIEDFEECNSNGSDCEFVPFASFSPAVEFTDCSVTSDGESVSLDDAQITQVIINNQDVTDCSVSGTTVSCSYV 260
               SCOP domains d2ifra_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.eeeeeee...eeeeeeeee..eee.eeeeeeeeeeee........eeeeeeeeee...eeeeeeee...eee.--.......eeeeeeeeee..eeeeeeee....eeeeeee...........eeeeeee..eee......eee....eee..eeeeeeeeee..eee.....eee..ee..ee.eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ifr A   1 TVESNWGGAILIGSDFDTVSATANVPSASGGSSAAGTAWVGIDGDTCQTAILQTGFDWYGDGTYDAWYEWYPEVSDDF--ITISEGDSIQMSVTATSDTSGSATLENLTTGQKVSKSFSNESSGSLCRTNAEFIIEDFEECNSNGSDCEFVPFASFSPAVEFTDCSVTSDGESVSLDDAQITQVIINNQDVTDCSVSGTTVSCSYV 206
                                    10        20        30        40        50        60        70       | -|       90       100       110       120       130       140       150       160       170       180       190       200      
                                                                                                        78 81                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .eee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2ifr B 501 xFKFxALRx 509
                            |   |   |
                          501-ACE   |
                              505-TA2
                                  509-NH2
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRTB_SCYLI | P15369)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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: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.
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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  3.4.23.32
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRTB_SCYLI | P15369: 1s2b 1s2k 2ifw

(-) Related Entries Specified in the PDB File

1s2b 1s2k