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(-) Description

Title :  STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE
 
Authors :  Z. Han, N. Sakai, R. Hilgenfeld
Date :  31 Oct 14  (Deposition) - 15 Apr 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Han, N. Sakai, L. H. Bottger, S. Klinke, J. Hauber, A. X. Trautwein, R. Hilgenfeld
Crystal Structure Of The Peroxo-Diiron(Iii) Intermediate Of Deoxyhypusine Hydroxylase, An Oxygenase Involved In Hypusination.
Structure V. 23 882 2015
PubMed-ID: 25865244  |  Reference-DOI: 10.1016/J.STR.2015.03.002

(-) Compounds

Molecule 1 - DEOXYHYPUSINE HYDROXYLASE
    Chains: A, B
    EC Number: 1.14.99.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PGEX-6P-1
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HDOHH, DEOXYHYPUSINE DIOXYGENASE, DEOXYHYPUSINE MONOOXYGENASE, HEAT-LIKE REPEAT-CONTAINING PROTEIN 1

 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  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2GAI5Ligand/IonGUANIDINE
3PER2Ligand/IonPEROXIDE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GAI4Ligand/IonGUANIDINE
3PER1Ligand/IonPEROXIDE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GAI1Ligand/IonGUANIDINE
3PER1Ligand/IonPEROXIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:89 , GLU A:90 , HIS A:207 , PER A:303 , HOH A:2001 , HOH A:2003BINDING SITE FOR RESIDUE FE A 301
02AC2SOFTWAREHIS A:56 , HIS A:240 , GLU A:241 , PER A:303 , HOH A:2002 , HOH A:2003BINDING SITE FOR RESIDUE FE A 302
03AC3SOFTWAREHIS A:56 , HIS A:89 , GLU A:90 , HIS A:207 , MET A:237 , HIS A:240 , GLU A:241 , FE A:301 , FE A:302 , HOH A:2003BINDING SITE FOR RESIDUE PER A 303
04AC4SOFTWAREGLU A:274 , LEU A:277 , ASP A:278 , HOH A:2227BINDING SITE FOR RESIDUE GAI A 404
05AC5SOFTWAREGLU A:4 , PRO A:37 , GLU A:188 , LEU B:145BINDING SITE FOR RESIDUE GAI A 405
06AC6SOFTWARETHR A:233 , GLU A:234 , HOH A:2255BINDING SITE FOR RESIDUE GAI A 406
07AC7SOFTWAREGLY A:36 , PRO A:37 , ILE A:40 , ASP A:67 , ARG A:69 , HOH A:2060BINDING SITE FOR RESIDUE GAI A 407
08AC8SOFTWAREHIS B:89 , GLU B:90 , HIS B:207 , FE B:302 , PER B:303 , HOH B:2001 , HOH B:2003BINDING SITE FOR RESIDUE FE B 301
09AC9SOFTWAREHIS B:56 , HIS B:240 , GLU B:241 , FE B:301 , PER B:303 , HOH B:2002 , HOH B:2003BINDING SITE FOR RESIDUE FE B 302
10BC1SOFTWAREHIS B:56 , MET B:86 , HIS B:89 , GLU B:90 , HIS B:207 , MET B:237 , HIS B:240 , GLU B:241 , FE B:301 , FE B:302 , HOH B:2003BINDING SITE FOR RESIDUE PER B 303
11BC2SOFTWARELEU A:145 , GLU B:4 , GLY B:36 , PRO B:37 , GLU B:188 , HOH B:2025BINDING SITE FOR RESIDUE GAI B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D50)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D50)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D50)

(-) Exons   (0, 0)

(no "Exon" information available for 4D50)

(-) 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d50 A  -5 GPLGSMVTEQEVDAIGQTLVDPKQPLQARFRALFTLRGLGGPGAIAWISQAFDDDSALLKHELAYCLGQMQDARAIPMLVDVLQDTRQEPMVRHEAGEALGAIGDPEVLEILKQYSSDPVIEVAETCQLAVRRLEWLQQHGGEPAAGPYLSVDPAPPAEERDVGRLREALLDESRPLFERYRAMFALRNAGGEEAALALAEGLHCGSALFRHEVGYVLGQLQHEAAVPQLAAALARCTENPMVRHECAEALGAIARPACLAALQAHADDPERVVRESCEVALDMYEHETG 285
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
                               -1|                                                                                                                                                                                                                                                                                            
                                 1                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d50 B  -5 GPLGSMVTEQEVDAIGQTLVDPKQPLQARFRALFTLRGLGGPGAIAWISQAFDDDSALLKHELAYCLGQMQDARAIPMLVDVLQDTRQEPMVRHEAGEALGAIGDPEVLEILKQYSSDPVIEVAETCQLAVRRLEWLQQHGGEPAAGPYLSVDPAPPAEERDVGRLREALLDESRPLFERYRAMFALRNAGGEEAALALAEGLHCGSALFRHEVGYVLGQLQHEAAVPQLAAALARCTENPMVRHECAEALGAIARPACLAALQAHADDPERVVRESCEVALDMYEHETG 285
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
                               -1|                                                                                                                                                                                                                                                                                            
                                 1
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  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 4D50)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D50)

(-) Gene Ontology  (9, 9)

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 Related Entries

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        DOHH_HUMAN | Q9BU89: 4d4z

(-) Related Entries Specified in the PDB File

4d4z STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE IN COMPLEX WITH GLYCEROL