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(-) Description

Title :  CRYSTAL STRUCTURE OF PUROMYCIN HYDROLASE
 
Authors :  Y. Matoba, M. Sugiyama
Date :  27 May 11  (Deposition) - 27 Jul 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pop Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, A. Nakayama, K. Oda, M. Noda, T. Kumagai, M. Nishimura, M. Sugiyama
Structural Evidence That Puromycin Hydrolase Is A New Type Of Aminopeptidase With A Prolyl Oligopeptidase Family Fold
Proteins V. 79 2999 2011
PubMed-ID: 21905123  |  Reference-DOI: 10.1002/PROT.23139

(-) Compounds

Molecule 1 - AMINOPEPTIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PMH
    Organism Scientific: STREPTOMYCES MOROOKAENSIS
    Organism Taxid: 1970
    Strain: JCM4673

 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  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:188 , HIS A:209 , HOH A:1078 , HOH A:1254 , HOH A:1685BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:261 , ALA A:276 , ALA A:277BINDING SITE FOR RESIDUE SO4 A 1003
3AC3SOFTWAREARG A:223 , THR A:225 , GLU A:226BINDING SITE FOR RESIDUE SO4 A 1004
4AC4SOFTWARETHR B:262 , ARG B:282 , HOH B:1879BINDING SITE FOR RESIDUE SO4 B 1002
5AC5SOFTWAREARG B:188 , HIS B:209 , HOH B:1203 , HOH B:1215 , HOH B:1473BINDING SITE FOR RESIDUE SO4 B 1005
6AC6SOFTWAREARG A:371 , ARG B:223 , THR B:225 , GLU B:226 , HOH B:1944BINDING SITE FOR RESIDUE SO4 B 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AZO)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:66 -Pro A:67
2His A:209 -Pro A:210
3Gly A:433 -Pro A:434
4Ala B:66 -Pro B:67
5His B:209 -Pro B:210
6Gly B:433 -Pro B:434

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AZO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AZO)

(-) Exons   (0, 0)

(no "Exon" information available for 3AZO)

(-) 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:661
 aligned with Q2HXD9_STRMO | Q2HXD9 from UniProtKB/TrEMBL  Length:662

    Alignment length:661
                                    11        21        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       591       601       611       621       631       641       651       661 
         Q2HXD9_STRMO     2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCMAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRMPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGMRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVMAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGSAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETMVRALEAELSLYAQVFGVEVAGVPLLKLGE 662
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........hhhhhhhh....eeeeee..eeeeeeee.....eeeeeee.....eee..........hhhhh....eeee.......eeeee......eeee..........ee..........eeeeeeeee....eeeeeeeee.......eeeeeeeee.......hhhhhee.......ee...ee.....eeeeeee.........eeeeeeee.....eeeeeeeeee....eeeeee.....eeeee......eeeee......eee...................eee.....eeeee.....eeeee......eee......eeeeeeeee..eeeeeeee..eeeeeeeee.....eeeee.......hhhhh...eeeeee.....eeeeeee......ee........eeeee............hhhhhhhhh...eeeeee.......hhhhhhh......hhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh....eeeee....hhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azo A   2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCmAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRmPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGmRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVmAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGSAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETmVRALEAELSLYAQVFGVEVAGVPLLKLGE 662
                                    11        21        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       591       601       611       621       631 |     641       651       661 
                                                                                                                                                                           147-MSE                                                          212-MSE                                                                             296-MSE                                                                                                                              429-MSE                                                                                                                                                                                                     633-MSE                         


Chain B from PDB  Type:PROTEIN  Length:661
 aligned with Q2HXD9_STRMO | Q2HXD9 from UniProtKB/TrEMBL  Length:662

    Alignment length:661
                                    11        21        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       591       601       611       621       631       641       651       661 
         Q2HXD9_STRMO     2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCMAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRMPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGMRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVMAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGSAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETMVRALEAELSLYAQVFGVEVAGVPLLKLGE 662
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........hhhhhhhh....eeeeee..eeeeeeee.....eeeeeee.....eee..........hhhhh....eeee.......eeeee......eeee..........ee..........eeeeeeeeehhh.eeeeeeeee.......eeeeeeeee.......hhhhhee.......ee...ee.....eeeeeee.........eeeeeeee.....eeeeeeeeee....eeeeee.....eeeee......eeeee......eee...................eee.....eeeee.....eeeeee....eeee......eeeeeeeee..eeeeeeee..eeeeeeeee.....eeeee.......hhhhh...eeeeee.....eeeeeee......ee........eeeee............hhhhhhhhh...eeeeee.......hhhhhhh......hhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh....eeeee....hhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azo B   2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCmAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRmPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGmRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVmAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGSAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETmVRALEAELSLYAQVFGVEVAGVPLLKLGE 662
                                    11        21        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       591       601       611       621       631 |     641       651       661 
                                                                                                                                                                           147-MSE                                                          212-MSE                                                                             296-MSE                                                                                                                              429-MSE                                                                                                                                                                                                     633-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3AZO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AZO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AZO)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2HXD9_STRMO | Q2HXD9)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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.

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  3azo
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 Related Entries

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

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        Q2HXD9_STRMO | Q2HXD9: 3azp 3azq

(-) Related Entries Specified in the PDB File

3azp 3azq