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(-) Description

Title :  STRUCTURE OF THE PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP WITH D-ARGININE BOUND
 
Authors :  N. R. Silvaggi, L. Han
Date :  01 Sep 15  (Deposition) - 25 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Aminotransferase, Hydroxylase, Enduracididine, Pyridoxal 5'- Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Han, A. W. Schwabacher, G. R. Moran, N. R. Silvaggi
Streptomyces Wadayamensis Mppp Is A Pyridoxal 5'-Phosphate-Dependent L-Arginine Alpha-Deaminase, Gamma-Hydroxylase In The Enduracididine Biosynthetic Pathway.
Biochemistry V. 54 7029 2015
PubMed-ID: 26551990  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01016

(-) Compounds

Molecule 1 - PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificSTREPTOMYCES WADAYAMENSIS
    Organism Taxid141454

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
15DK4Ligand/Ion(E)-N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-D-ARGININE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15DK2Ligand/Ion(E)-N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-D-ARGININE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15DK2Ligand/Ion(E)-N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-D-ARGININE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
15DK4Ligand/Ion(E)-N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-D-ARGININE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , GLY A:28 , HIS A:29 , SER A:89 , SER A:90 , SER A:91 , PHE A:115 , THR A:156 , ASN A:160 , ASP A:188 , SER A:190 , PHE A:191 , LYS A:221 , ASP A:227 , LYS A:229 , ARG A:352 , HOH A:601 , HOH A:605 , HOH A:615 , HOH A:736 , LEU C:252binding site for residue 5DK A 500
2AC2SOFTWAREASP B:27 , GLY B:28 , HIS B:29 , SER B:89 , SER B:90 , SER B:91 , PHE B:115 , THR B:156 , ASN B:160 , ASP B:188 , SER B:190 , PHE B:191 , LYS B:221 , ASP B:227 , LYS B:229 , ARG B:352 , HOH B:503 , HOH B:518 , HOH B:519 , LEU D:252binding site for residue 5DK B 401
3AC3SOFTWAREASP B:116 , ASP B:120 , HOH B:521 , HOH B:532 , HOH B:653 , HOH C:702binding site for residue MG B 402
4AC4SOFTWAREHOH A:640 , ASP C:27 , GLY C:28 , HIS C:29 , SER C:89 , SER C:90 , SER C:91 , PHE C:115 , THR C:156 , ASN C:160 , ASP C:188 , PHE C:191 , LYS C:221 , ASP C:227 , LYS C:229 , ARG C:352 , HOH C:604 , HOH C:618 , HOH C:636 , HOH C:668binding site for residue 5DK C 500
5AC5SOFTWARELEU B:252 , ASP D:27 , GLY D:28 , HIS D:29 , SER D:89 , SER D:90 , SER D:91 , PHE D:115 , THR D:156 , ASN D:160 , ASP D:188 , PHE D:191 , LYS D:221 , ASP D:227 , LYS D:229 , ARG D:352 , HOH D:628 , HOH D:630 , HOH D:635binding site for residue 5DK D 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DJ3)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1His A:112 -Pro A:113
2Thr A:157 -Pro A:158
3Asn A:160 -Pro A:161
4Glu A:296 -Gly A:297
5His B:112 -Pro B:113
6Thr B:157 -Pro B:158
7Asn B:160 -Pro B:161
8Glu B:296 -Gly B:297
9His C:112 -Pro C:113
10Thr C:157 -Pro C:158
11Asn C:160 -Pro C:161
12Glu C:296 -Gly C:297
13His D:112 -Pro D:113
14Thr D:157 -Pro D:158
15Asn D:160 -Pro D:161
16Glu D:296 -Gly D:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 5DJ3)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........eeeeee...hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj3 A  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVL 373
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 

Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........eeeeee...hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj3 B  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVL 373
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 

Chain C from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh..eeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........eeeeee...hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj3 C  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVL 373
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 

Chain D from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........eeeeee...hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj3 D  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVL 373
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 

   Legend:   → Mismatch (orange background)
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    → 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 5DJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DJ3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DJ3)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0X1KHF5_9 | A0A0X1KHF55dj1

(-) Related Entries Specified in the PDB File

5dj1 5DJ1 CONTAINS THE UNLIGANDED HOLOENZYME