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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTATION OF AN ACYLPTIDE HYDROLASE/ESTERASE FROM AEROPYRUM PERNIX K1
 
Authors :  H. F. Zhang, B. S. Zheng, Z. Rao
Date :  17 Aug 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Crystal Structure, Truncated, Acylpeptide Hydrolase, Aeropyrum Pernix K1, Cytoplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. F. Zhang, B. S. Zheng, Z. Rao
Expression, Purification And Crystal Structure Of A Truncated Acylpeptide Hydrolase From Aeropyrum Pernix K1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACYLAMINO-ACID-RELEASING ENZYME
    ChainsA, B
    EC Number3.4.19.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 21-582
    Organism ScientificAEROPYRUM PERNIX
    Organism Taxid56636
    SynonymAARE, ACYL-PEPTIDE HYDROLASE, APH, ACYLAMINOACYL- PEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QZP)

(-) Sites  (0, 0)

(no "Site" information available for 2QZP)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:416 -A:453
2B:416 -B:453

(-) Cis Peptide Bonds  (6, 6)

Asymmetric 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 2QZP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QZP)

(-) Sequences/Alignments

Asymmetric 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:560
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:560
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581
           APEH_AERPE    22 VEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
               SCOP domains d2qzpa1 A:22-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                         d2qzpa2 A:322-581 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeee......eeeee.....ee.......ee.ee......eeeeee.......eeeeee.................eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee......eee....eeeeeee......eeeeeee...eeeeee......eee......hhhhhh.....eeee.....eeeeeee..eeeeee..eee..........eee..eeee..........eee.....eee...............eeeeee.....eeeeeee........eeeeeee............hhhhhhhhhh..eeeee........hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhh......eeeee....hhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzp A  22 VEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581

Chain B from PDB  Type:PROTEIN  Length:561
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:561
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580 
           APEH_AERPE    21 AVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
               SCOP domains -d2qzpb1 B:22-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                         d2qzpb2 B:322-581 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_S9-2qzpB01 B:376-579                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_S9-2qzpB02 B:376-579                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ...ee..........eeeeee.....eeeee..............ee.ee.....eeeeeee.......eeeeeee.......ee.......ee...ee....eeeeee....eeeeeee..eeeeeeee..eeeeeeee..eeeeeeeee..eeeee..........ee....eee...ee.....ee..eee...ee............................eeeeee.....eeeeeee..eeeeee..ee...........ee....eeeeeee..eeeeeee....eeee.....hhhhhh....eeeee.......eeeeee........eeeee..............hhhhhhhhhh..eeeee........hhhhhh.......hhhhhhhhhhhhhhhhh..eee.eeeeehhhhhhhhhhhhhh.....eeeee.....hhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh...eeeeee................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzp B  21 AVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580 

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (4, 4)

Asymmetric 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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  Cis Peptide Bonds
    Gly A:369 - Pro A:370   [ RasMol ]  
    Gly B:369 - Pro B:370   [ RasMol ]  
    Leu A:311 - Pro A:312   [ RasMol ]  
    Leu B:311 - Pro B:312   [ RasMol ]  
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    Thr B:358 - Pro B:359   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        APEH_AERPE | Q9YBQ21ve6 1ve7 2hu5 2hu7 2hu8 2qr5 3o4g 3o4h 3o4i 3o4j 4re5 4re6

(-) Related Entries Specified in the PDB File

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