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(-) Description

Title :  ACYLAMINOACYL PEPTIDASE COMPLEXED WITH A CHLOROMETHYLKETONE INHIBITOR
 
Authors :  D. K. Menyhard, Z. Orgovan, Z. Szeltner, I. Szamosi, V. Harmat
Date :  22 Sep 14  (Deposition) - 28 Jan 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Propeller, Alpha-Beta-Hydrolase Fold, Chloromethyl-Ketone Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Menyhard, Z. Orgovan, Z. Szeltner, I. Szamosi, V. Harmat
Catalytically Distinct States Captured In A Crystal Lattice The Substrate-Bound And Scavenger States Of Acylaminoacyl Peptidase And Their Implications For Functionality.
Acta Crystallogr. , Sect. D V. 71 461 2015
PubMed-ID: 25760596  |  Reference-DOI: 10.1107/S1399004714026819

(-) Compounds

Molecule 1 - ACYLAMINO-ACID-RELEASING ENZYME
    Chains: A, B
    EC Number: 3.4.19.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE_1547.1
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
    Synonym: AARE, ACYL-PEPTIDE HYDROLASE, APH, ACYLAMINOACYL-PEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4Y3A2Ligand/IonN-[(BENZYLOXY)CARBONYL]GLYCYL-N-[(2S,3R)-4-CHLORO-3-HYDROXY-1-PHENYLBUTAN-2-YL]GLYCINAMIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:368 , GLY A:369 , SER A:445 , TYR A:446 , PHE A:485 , PHE A:488 , ARG A:526 , HIS A:556 , HOH A:1130BINDING SITE FOR RESIDUE Y3A A 601
2AC2SOFTWAREARG A:277 , HOH A:837 , HOH A:848BINDING SITE FOR RESIDUE ACT A 602
3AC3SOFTWARETRP A:337 , ARG A:345 , TYR A:403 , TRP A:407 , HOH A:807BINDING SITE FOR RESIDUE MPD A 603
4AC4SOFTWAREGLY B:368 , GLY B:369 , SER B:445 , TYR B:446 , PHE B:485 , ARG B:526 , HIS B:556BINDING SITE FOR RESIDUE Y3A B 601
5AC5SOFTWAREASN B:65 , SER B:66 , ILE B:114 , HOH B:708BINDING SITE FOR RESIDUE MPD B 602
6AC6SOFTWAREHIS A:549 , LEU A:569 , PHE A:573 , HIS B:549 , PRO B:570 , HOH B:748BINDING SITE FOR RESIDUE MPD B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RE5)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:311 -Pro A:312
2Thr A:358 -Pro A:359
3Gly A:369 -Pro A:370
4Leu B:311 -Pro B:312
5Thr B:358 -Pro B:359
6Gly B:369 -Pro B:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RE5)

(-) Exons   (0, 0)

(no "Exon" information available for 4RE5)

(-) 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:574
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.eeeeeeee...eeeeeeee..eeeeeee.....ee.......ee.ee.....eeeeeee.......eeeeeee......eee.......eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee......eee....eeeeeeee.....eeeeeee...eeeeee......eee.....hhhhhhh..eeeeeee.....eeeeeee..eeeeee..eee.....eeeeeeee..eeeeeeee..eeeeeeee....eee....hhhhhhheeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4re5 A   8 EFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577    


Chain B from PDB  Type:PROTEIN  Length:574
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee...eeeeeeee..eeeeeee....eee.......ee.ee.....eeeeeee.......eeeeeee......eee.......eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee......eee....eeeeeeee.....eeeeeee...eeeeee......eee.....hhhhhhh..eeeeeee.....eeeeeee..eeeeee..eee.....eeeeeeee..eeeeeeee..eeeeeeee....eee....hhhhhh.eeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4re5 B   8 EFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577
   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 4RE5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RE5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RE5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/Swiss-Prot
        APEH_AERPE | Q9YBQ2: 1ve6 1ve7 2hu5 2hu7 2hu8 2qr5 2qzp 3o4g 3o4h 3o4i 3o4j 4re6

(-) Related Entries Specified in the PDB File

4re6