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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVE SITE F1-MUTANT E213Q SOAKED WITH PEPTIDE ALA-PHE
 
Authors :  P. Goettig, H. Brandstetter, M. Groll, W. Goehring, P. V. Konarev, D. I. R. Huber, J. -S. Kim
Date :  15 Oct 04  (Deposition) - 12 Jul 05  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Hydrolase, Caged Active Site, Substrate Recognition, Hydrogen Bonded Network, Peptide Cleavage, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Goettig, H. Brandstetter, M. Groll, W. Goehring, P. V. Konarev, D. I. Svergun, R. Huber, J. -S. Kim
X-Ray Snapshots Of Peptide Processing In Mutants Of Tricorn-Interacting Factor F1 From Thermoplasma Acidophilum
J. Biol. Chem. V. 280 33387 2005
PubMed-ID: 15994304  |  Reference-DOI: 10.1074/JBC.M505030200

(-) Compounds

Molecule 1 - PROLINE IMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET6C
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TA0830
    Mutation: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: PIP, PROLYL AMINOPEPTIDASE, PAP, TRICORN PROTEASE INTERACTING FACTOR F1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2PHE2Mod. Amino AcidPHENYLALANINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:37 , MET A:40 , SER A:105 , TYR A:106 , TYR A:205 , ASN A:209 , GLN A:213 , ILE A:216 , GLU A:245 , HIS A:271BINDING SITE FOR RESIDUE PHE A 300
2AC2SOFTWARELEU A:196 , PHE A:302BINDING SITE FOR RESIDUE ALA A 301
3AC3SOFTWAREGLU A:4 , ARG A:49 , ALA A:301BINDING SITE FOR RESIDUE PHE A 302

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:22

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:37 -Pro A:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XRM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XRM)

(-) Exons   (0, 0)

(no "Exon" information available for 1XRM)

(-) 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:293
 aligned with PIP_THEAC | P96084 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:293
                                                                                                                                                                                                                                                                                                                           293   
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
            PIP_THEAC     4 ECIENYAKVNGIYIYYKLCKAPEEKAKLMTMHGGPGMSHDYLLSLRDMTKEGITVLFYDQFGCGRSEEPDQSKFTIDYGVEEAEALRSKLFGNEKVFLMGSSYGGALALAYAVKYQDHLKGLIVSGGLSSVPLTVKEMNRLIDELPAKYRDAIKKYGSSGSYENPEYQEAVNYFYHQHLLRSEDWPPEVLKSLEYAERRNVYRIMNGPNEFTITGTIKDWDITDKISAIKIPTLITVGEYDEVTPNVARVIHEKIAGSELHVFRDCSHLTMWEDREGYNKLLSDFILKHL---   -
               SCOP domains d1xrma_ A: Tricorn interacting factor F1                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xrmA00 A:4-293  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                             --- CATH domains
               Pfam domains ---------------------------Abhydrolase_6-1xrmA01 A:31-284                                                                                                                                                                                                                                ------------ Pfam domains
         Sec.struct. author ..eee..ee..ee.eeeee......eeeeee......hhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhh..................hhhhh...eeeeee.....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xrm A   4 ECIENYAKVNGIYIYYKLCKAPEEKAKLMTMHGGPGMSHDYLLSLRDMTKEGITVLFYDQFGCGRSEEPDQSKFTIDYGVEEAEALRSKLFGNEKVFLMGSSYGGALALAYAVKYQDHLKGLIVSGGLSSVPLTVKEMNRLIDELPAKYRDAIKKYGSSGSYENPEYQEAVNYFYHQHLLRSEDWPPEVLKSLEYAERRNVYRIMNGPNQFTITGTIKDWDITDKISAIKIPTLITVGEYDEVTPNVARVIHEKIAGSELHVFRDCSHLTMWEDREGYNKLLSDFILKHLFAF 302
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293|  
                                                                                                                                                                                                                                                                                                                           293|  
                                                                                                                                                                                                                                                                                                                            300
   Legend:   → Mismatch (orange background)
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  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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIP_THEAC | P96084)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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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  1xrm
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  PIP_THEAC | P96084
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  3.4.11.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        PIP_THEAC | P96084: 1mt3 1mtz 1mu0 1xqv 1xqw 1xqx 1xqy 1xrl 1xrn 1xro 1xrp 1xrq 1xrr

(-) Related Entries Specified in the PDB File

1mt3 CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR SELENOMETHIONINE-F1
1mtz CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR F1
1mu0 CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR F1 COMPLEX WITH PCK
1xqv THE SAME PROTEIN G37A MUTANT
1xqw THE SAME PROTEIN S105A MUTANT COMPLEX WITH PHE-LEU
1xqx THE SAME PROTEIN S105A MUTANT COMPLEX WITH PCK
1xqy THE SAME PROTEIN S105A MUTANT COMPLEX WITH PRO-LEU-GLY-GLY
1xrl THE SAME PROTEIN Y205F MUTANT COMPLEX WITH INHIBITOR PCK
1xrn THE SAME PROTEIN E213Q MUTANT SOAKED WITH PEPTIDE PHE-ALA
1xro THE SAME PROTEIN E213Q MUTANT SOAKED WITH PEPTIDE PHE-LEU
1xrp THE SAME PROTEIN E213Q MUTANT SOAKED WITH PEPTIDE PRO-LEU- GLY-GLY
1xrq THE SAME PROTEIN E245Q MUTANT SOAKED WITH PEPTIDE PHE-LEU
1xrr THE SAME PROTEIN E245Q MUTANT SOAKED WITH PEPTIDE PRO-PRO