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(-) Description

Title :  CRYSTAL STRUCTURE OF ACETYLPOLYAMINE AMIDOHYDROLASE FROM MYCOPLANA RAMOSA IN COMPLEX WITH A THIOL INHIBITOR
 
Authors :  C. Decroos, D. W. Christianson
Date :  17 May 15  (Deposition) - 29 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acetylpolyamine Amidohydrolase, Arginase Fold, Enzyme-Inhibitor Complex, Polyamine, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Decroos, D. W. Christianson
Design, Synthesis, And Evaluation Of Polyamine Deacetylase Inhibitors, And High-Resolution Crystal Structures Of Their Complexes With Acetylpolyamine Amidohydrolase.
Biochemistry V. 54 4692 2015
PubMed-ID: 26200446  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00536

(-) Compounds

Molecule 1 - ACETYLPOLYAMINE AMINOHYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APHA, APH
    Organism Scientific: MYCOPLANA RAMOSA
    Organism Taxid: 40837

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2K2Ligand/IonPOTASSIUM ION
3NA2Ligand/IonSODIUM ION
4SS92Ligand/Ion5-[(3-AMINOPROPYL)AMINO]PENTANE-1-THIOL
5ZN4Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:19 , HIS A:158 , HIS A:159 , GLY A:167 , TYR A:168 , ASP A:195 , HIS A:197 , ASP A:284 , ILE A:291 , TYR A:323 , ZN A:404 , ZN A:405 , HOH A:513 , HOH A:542 , HOH A:546 , HOH A:662 , HOH A:793 , TYR B:83 , GLU B:106binding site for residue SS9 A 401
02AC2SOFTWAREASP A:193 , ASP A:195 , HIS A:197 , SER A:216 , LEU A:217binding site for residue K A 402
03AC3SOFTWAREPHE A:206 , ARG A:209 , VAL A:212 , THR A:243 , HOH A:706binding site for residue NA A 403
04AC4SOFTWAREASP A:195 , HIS A:197 , ASP A:284 , SS9 A:401 , ZN A:405binding site for residue ZN A 404
05AC5SOFTWAREHIS A:158 , HIS A:159 , SS9 A:401 , ZN A:404 , HOH A:793binding site for residue ZN A 405
06AC6SOFTWARELYS A:15 , TRP A:75 , LYS A:84 , GLY A:85 , HOH A:514binding site for residue GOL A 406
07AC7SOFTWAREASP B:193 , ASP B:195 , HIS B:197 , SER B:216 , LEU B:217binding site for residue K B 401
08AC8SOFTWAREPHE B:206 , ARG B:209 , VAL B:212 , THR B:243 , HOH B:673binding site for residue NA B 402
09AC9SOFTWAREASP B:195 , HIS B:197 , ASP B:284 , ZN B:404 , SS9 B:405binding site for residue ZN B 403
10AD1SOFTWAREHIS B:158 , HIS B:159 , ZN B:403 , SS9 B:405 , HOH B:804binding site for residue ZN B 404
11AD2SOFTWARETYR A:83 , GLU A:106 , HIS B:158 , HIS B:159 , GLY B:167 , TYR B:168 , ASP B:195 , HIS B:197 , PHE B:225 , ASP B:284 , GLY B:321 , TYR B:323 , ZN B:403 , ZN B:404 , HOH B:504 , HOH B:513 , HOH B:534 , HOH B:553 , HOH B:804binding site for residue SS9 B 405
12AD3SOFTWARELYS B:15 , TRP B:75 , LYS B:84 , GLY B:85 , HOH B:523binding site for residue GOL B 406
13AD4SOFTWAREHOH A:567 , ARG B:96 , SER B:98 , HOH B:743binding site for residue GOL B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:154 -Pro A:155
2Phe A:225 -Pro A:226
3Arg B:154 -Pro B:155
4Phe B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZUN)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhh....eee..eee.....hhhhhhhhhhhhhh....ee........hhhhh.hhhhhhhhhhhhhhhhhh......................hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh...eeee....................hhhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeeeeeee.................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zun A   1 MRVIFSEDHKLRNAKTELYGGELVPPFEAPFRAEWILAAVKEAGFDDVVAPARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGADLIAAGHKAAFSLCRPPGHHAGIDMFGGYCFINNAAVAAQRLLDKGAKKIAILDVDFHHGNGTQDIFYERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMGRGTPYSVWGEALTDSLKRIAAFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAASGVPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
                                    10        20        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 


Chain B from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhh....eee..eee.....hhhhhhhhhhhhhh....ee........hhhhh.hhhhhhhhhhhhhhhhhh......................hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh...eeee....................hhhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeeeeeee.................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zun B   1 MRVIFSEDHKLRNAKTELYGGELVPPFEAPFRAEWILAAVKEAGFDDVVAPARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGADLIAAGHKAAFSLCRPPGHHAGIDMFGGYCFINNAAVAAQRLLDKGAKKIAILDVDFHHGNGTQDIFYERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMGRGTPYSVWGEALTDSLKRIAAFGAEAIVVSLGVDTFEQDPISFFKLTSPDYITMGRTIAASGVPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
                                    10        20        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
   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 4ZUN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        APAH_MYCRA | Q48935: 3q9b 3q9c 3q9e 3q9f 4zum 4zuo 4zup 4zuq 4zur

(-) Related Entries Specified in the PDB File

4zum 4zuo 4zup 4zuq 4zur