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(-) Description

Title :  CRYSTAL STRUCTURE OF ACETYLPOLYAMINE AMIDOHYDROLASE FROM MYCOPLANA RAMOSA IN COMPLEX WITH A HYDROXAMATE 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 :  1.42
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, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
15XA2Ligand/Ion5-AMINO-N-HYDROXYPENTANAMIDE
2GOL4Ligand/IonGLYCEROL
3K4Ligand/IonPOTASSIUM ION
4NO34Ligand/IonNITRATE ION
5ZN4Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:195 , HIS A:197 , ASP A:284 , 5XA A:405binding site for residue ZN A 401
02AC2SOFTWAREHIS A:146 , NO3 A:408binding site for residue ZN A 402
03AC3SOFTWAREASP A:193 , ASP A:195 , HIS A:197 , SER A:216 , LEU A:217binding site for residue K A 403
04AC4SOFTWAREPHE A:206 , ARG A:209 , VAL A:212 , THR A:243 , HOH A:609binding site for residue K A 404
05AC5SOFTWAREGLU A:117 , HIS A:158 , HIS A:159 , TYR A:168 , ASP A:195 , HIS A:197 , PHE A:225 , ASP A:284 , TYR A:323 , ZN A:401 , HOH A:729 , HOH B:646binding site for residue 5XA A 405
06AC6SOFTWARELYS A:15 , TRP A:75 , LYS A:84 , GLY A:85 , HOH A:531 , HOH A:712binding site for residue GOL A 406
07AC7SOFTWAREMET A:1 , PHE A:45 , ALA A:340 , NO3 A:408 , HOH A:504 , HOH A:536 , HOH A:557binding site for residue NO3 A 407
08AC8SOFTWAREMET A:1 , HIS A:146 , LYS A:147 , ALA A:148 , ZN A:402 , NO3 A:407 , HOH A:557 , HOH A:564 , HOH A:755binding site for residue NO3 A 408
09AC9SOFTWARETYR A:231 , ALA A:232 , GLU A:233 , HOH A:513 , HOH A:554 , HOH A:769 , ARG B:100binding site for residue GOL A 409
10AD1SOFTWAREASP B:195 , HIS B:197 , ASP B:284 , 5XA B:405binding site for residue ZN B 401
11AD2SOFTWAREHIS B:146 , NO3 B:408binding site for residue ZN B 402
12AD3SOFTWAREASP B:193 , ASP B:195 , HIS B:197 , SER B:216 , LEU B:217binding site for residue K B 403
13AD4SOFTWAREPHE B:206 , ARG B:209 , VAL B:212 , THR B:243 , HOH B:610binding site for residue K B 404
14AD5SOFTWAREGLU B:117 , HIS B:158 , HIS B:159 , GLY B:167 , TYR B:168 , ASP B:195 , HIS B:197 , PHE B:225 , ASP B:284 , TYR B:323 , ZN B:401 , HOH B:536 , HOH B:751binding site for residue 5XA B 405
15AD6SOFTWAREHOH A:529 , HOH A:559 , ARG B:96 , HOH B:502 , HOH B:765 , HOH B:789binding site for residue GOL B 406
16AD7SOFTWAREMET B:1 , PHE B:45 , ALA B:340 , NO3 B:408 , HOH B:513 , HOH B:544 , HOH B:562binding site for residue NO3 B 407
17AD8SOFTWAREMET B:1 , HIS B:146 , LYS B:147 , ALA B:148 , ZN B:402 , NO3 B:407 , HOH B:501 , HOH B:562 , HOH B:700binding site for residue NO3 B 408
18AD9SOFTWARELEU B:266 , THR B:307 , ALA B:310 , SER B:311 , HOH B:512 , HOH B:531 , HOH B:566 , HOH B:723 , HOH B:793 , HOH B:868binding site for residue GOL B 409

(-) SS Bonds  (0, 0)

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

(-) 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 4ZUP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZUP)

(-) 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
                 4zup 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..........hhhhhhhhhhhhhhhhhhhhhhh..eeee....................hhhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeeeeeee.................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zup 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)
  - → 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 4ZUP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4zun 4zuo 4zuq 4zur

(-) Related Entries Specified in the PDB File

4zum 4zun 4zuo 4zuq 4zur