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(-) Description

Title :  BINDING OF INHIBITORS BY ACYLAMINOACYL-PEPTIDASE
 
Authors :  A. L. Kiss, B. Hornung, K. Radi, Z. Gengeliczki, B. Sztaray, V. Harmat, L
Date :  26 Jul 06  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Hydrolase, Beta-Propeller, Enzyme-Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Kiss, B. Hornung, K. Radi, Z. Gengeliczki, B. Sztaray, T. Juhasz, Z. Szeltner, V. Harmat, L. Polgar
The Acylaminoacyl Peptidase From Aeropyrum Pernix K1 Though To Be An Exopeptidase Displays Endopeptidase Activity
J. Mol. Biol. V. 368 509 2007
PubMed-ID: 17350041  |  Reference-DOI: 10.1016/J.JMB.2007.02.025
(for further references see the PDB file header)

(-) 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
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    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  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2GOL5Ligand/IonGLYCEROL
3PHE2Mod. Amino AcidPHENYLALANINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:485 , ARG A:526 , PHE A:1002BINDING SITE FOR RESIDUE GLY A 1001
2AC2SOFTWAREGLY A:368 , GLY A:369 , SER A:445 , TYR A:446 , MET A:477 , PHE A:485 , ARG A:526 , THR A:527 , HIS A:556 , GLY A:1001BINDING SITE FOR RESIDUE PHE A 1002
3AC3SOFTWAREARG B:526 , PHE B:2002BINDING SITE FOR RESIDUE GLY B 2001
4AC4SOFTWAREGLY B:368 , GLY B:369 , SER B:445 , TYR B:446 , PHE B:485 , ARG B:526 , THR B:527 , GLY B:2001BINDING SITE FOR RESIDUE PHE B 2002
5AC5SOFTWAREPRO A:151 , PHE A:170 , TYR B:478 , GLU B:490 , THR B:493 , GLY B:495 , ARG B:497 , MET B:500BINDING SITE FOR RESIDUE GOL B 3001
6AC6SOFTWAREARG B:76 , LYS B:94 , LEU B:106 , GLU B:122 , LEU B:139BINDING SITE FOR RESIDUE GOL B 3002
7AC7SOFTWARETHR A:179 , SER A:180 , ASN A:181 , ARG A:188 , PRO A:225 , ARG A:226BINDING SITE FOR RESIDUE GOL A 3003
8AC8SOFTWAREARG A:76 , LYS A:94 , LEU A:106 , GLU A:122 , ALA A:123 , LEU A:139 , ASP A:140BINDING SITE FOR RESIDUE GOL A 3005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HU5)

(-) 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 2HU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HU5)

(-) Exons   (0, 0)

(no "Exon" information available for 2HU5)

(-) 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:575
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:575
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       582 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578   | 
          APEH_AERPE      9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERR-    -
               SCOP domains d2hu5a1 A:9-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                                       d2hu5a2 A:322-581 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeeeee...eeeeeeee..eeeeeee.....ee.......ee.ee.....eeeeeee.......eeeeeee.......ee.......eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee...eeeeee....eeeeeeee.....eeeeeee...eeeeee......eee.....hhhhhhh..eeeeeee.....eeeeeee..eeeeee..eee.....eeeeeeee..eeeeeeee..eeeeeeee....eee....hhhhhhheeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2hu5 A    9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERGF 1002
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578  || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      581| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      1001 


Chain B from PDB  Type:PROTEIN  Length:577
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:577
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        582  
                                    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    |  
          APEH_AERPE      8 EFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERR--    -
               SCOP domains d2hu5b1 B:8-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                                        d2hu5b2 B:322-582 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                 -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.eeeeeeee...eeeeeeee..eeeeeee....eee.......ee.ee.....eeeeeee.......eeeeeee......eee.......eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee...eeeeee.....eeeeeee.....eeeeee....eeeeee......eee.....hhhhhhh..eeeeeee.....eeeeeee..eeeeee..eee.....eeeeeeee..eeeeeeee..eeeeeeee....eee....hhhhhhheeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2hu5 B    8 EFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERRGF 2002
                                    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    || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        582| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        2001
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HU5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (APEH_AERPE | Q9YBQ2)
molecular function
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2hu5
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  3.4.19.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        APEH_AERPE | Q9YBQ2: 1ve6 1ve7 2hu7 2hu8 2qr5 2qzp 3o4g 3o4h 3o4i 3o4j 4re5 4re6

(-) Related Entries Specified in the PDB File

2hu7 2hu8