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(-) Description

Title :  CRYSTAL STRUCTURE OF PUROMYCIN HYDROLASE S511A MUTANT COMPLEXED WITH PGG
 
Authors :  Y. Matoba, M. Sugiyama
Date :  27 May 11  (Deposition) - 27 Jul 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (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: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PMH
    Mutation: YES
    Organism Scientific: STREPTOMYCES MOROOKAENSIS
    Organism Taxid: 1970
    Strain: JCM4673
 
Molecule 2 - TRIPEPTIDE PGG
    Chains: C, D
    Engineered: YES
    Other Details: PURCHASED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:188 , HIS A:209 , HOH A:1127 , HOH A:1185BINDING SITE FOR RESIDUE SO4 A 1001
02AC2SOFTWAREARG A:261 , GLY A:275 , ALA A:276 , ALA A:277BINDING SITE FOR RESIDUE SO4 A 1003
03AC3SOFTWAREARG A:223 , THR A:225 , GLU A:226 , HOH A:1199BINDING SITE FOR RESIDUE SO4 A 1004
04AC4SOFTWAREHIS A:407 , ARG A:437 , ASN A:460 , TYR A:467BINDING SITE FOR RESIDUE SO4 A 1006
05AC5SOFTWARELEU A:18 , SER A:21 , ARG A:22 , ARG A:402 , GLU A:403 , ARG A:474BINDING SITE FOR RESIDUE SO4 A 1008
06AC6SOFTWAREARG A:25 , ALA A:27 , CYS A:28 , ALA A:340 , THR A:341BINDING SITE FOR RESIDUE SO4 A 1009
07AC7SOFTWARETHR B:262 , ARG B:282BINDING SITE FOR RESIDUE SO4 B 1002
08AC8SOFTWAREARG B:188 , HIS B:209 , HOH B:1177BINDING SITE FOR RESIDUE SO4 B 1005
09AC9SOFTWAREARG A:371 , ARG B:223 , THR B:225 , GLU B:226BINDING SITE FOR RESIDUE SO4 B 1007
10BC1SOFTWAREARG B:553BINDING SITE FOR RESIDUE SO4 B 1010

(-) SS Bonds  (0, 0)

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

(-) 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 3AZQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AZQ)

(-) 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..........eeeeeeeeehhh.eeeeeeeee.......eeeeeeeee.......hhhhhee.......ee...ee.....eeeeeee..........eeeeeee.....eeeeeeeee.....eeeeee.....eeeee......eeeee......eee...................eee.....eeeee.....eeeee......eee......eeeeeeeee..eeeeeee......eeeeee.....eeeee.......hhhhh...eeeeee.....eeeeeee......ee........eeeee............hhhhhhhhh...eeeeee.......hhhhhhh......hhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhh.....eeeee....hhhhhhh...hhhhhhhhhhhh.......hhhhhh.hhhhhhhh...eeeeee.......hhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azq A   2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCMAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRMPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGMRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVMAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGAAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETMVRALEAELSLYAQVFGVEVAGVPLLKLGE 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 


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.....eeeee......eee......eeeeeeeee..eeeeeeee..eeeeeeeee.....eeeee.......hhhhh...eeeeee.....eeeeeee......ee........eeeee............hhhhhhhhh...eeeeee.......hhhhhhh......hhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh....eeeee....hhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azq B   2 VSTAPYGAWQSPIDAALVASRSGRPACVGAVGDEVWWVAPRPAEAGRATLVRRRADGAEESALPAPWNVRNRVFEYSGFPWAGVPRPAGGPLLVFTHFGDQRLYAFEPDAPGGAVPRPLTPVSAVGGGLRWADPVLLPERGEVWCMAEEFTGEGPSDVRRFLAAVPLDGSAAADRSAVRELSDDAHRFVTGPRLSPDGRQAVWLAWDHPRMPWEGTELKTARVTEDGRFADTRTLLGGPEEAIAQAEWAPDGSLIVATDRTGWWNLHRVDPATGAATQLCRREEEFAGPLWTPGMRWFAPLANGLIAVVHGKGAAVLGILDPESGELVDAAGPWTEWAATLTVSGTRAVGVAASPRTAYEVVELDTVTGRARTIGARHTDPVDPAYYPEPQIRTFTAPDGREIHAHIYPPHSPDFTGPADELPPYVVMAHGGPTSRVPAVLDLDVAYFTSRGIGVADVNYGGSTGYGRAYRERLRGRWGVVDVEDCAAVATALAEEGTADRARLAVRGGAAGGWTAASSLVSTDVYACGTVLYPVLDLLGWADGGTHDFESRYLDFLIGSFEEFPERYRDRAPLTRADRVRVPFLLLQGLEDPVCPPEQCDRFLEAVAGCGVPHAYLSFEGEGHGFRRKETMVRALEAELSLYAQVFGVEVAGVPLLKLGE 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 


Chain C from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 3azq C   1 PG   2


Chain D from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 3azq D   1 PG   2
   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 3AZQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  3azq
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 Related Entries

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

UniProtKB/TrEMBL
        Q2HXD9_STRMO | Q2HXD9: 3azo 3azp

(-) Related Entries Specified in the PDB File

3azo 3azp