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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN OGFOD1, 2-OXOGLUTARATE AND IRON-DEPENDENT OXYGENASE DOMAIN CONTAINING 1, IN COMPLEX WITH N-OXALYLGLYCINE (NOG)
 
Authors :  S. Horita, M. A. Mcdonough, C. J. Schofield
Date :  05 Nov 13  (Deposition) - 19 Nov 14  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Jelly-Roll Fold, Translation, Ribosome, Double-Stranded Beta Helix, Oxygen Sensing, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Horita, J. S. Scotti, C. Thinnes, Y. S. Mottaghi-Taromsari, A. Thalhammer, W. Ge, W. Aik, C. Loenarz, C. J. Schofield, M. A. Mcdonough
Structure Of The Ribosomal Oxygenase Ogfod1 Provides Insights Into The Regio- And Stereoselectivity Of Prolyl Hydroxylases.
Structure V. 23 639 2015
PubMed-ID: 25728928  |  Reference-DOI: 10.1016/J.STR.2015.01.014

(-) Compounds

Molecule 1 - 2-OXOGLUTARATE AND IRON-DEPENDENT OXYGENASE DOMAIN- CONTAINING PROTEIN 1
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OGFOD1, KIAA1612, TPA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TERMINATION AND POLYADENYLATION 1 HOMOLOG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN1Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION
4OGA1Ligand/IonN-OXALYLGLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:155 , ASP A:157 , HIS A:218 , OGA A:603 , HOH A:841BINDING SITE FOR RESIDUE MN A 601
2AC2SOFTWAREARG A:108 , ASP A:506 , THR A:509 , HOH A:944BINDING SITE FOR RESIDUE NA A 602
3AC3SOFTWARELEU A:152 , HIS A:155 , ASP A:157 , TYR A:169 , HIS A:218 , VAL A:220 , ARG A:230 , MN A:601 , GOL A:604 , HOH A:838 , HOH A:841 , HOH A:843 , HOH A:844BINDING SITE FOR RESIDUE OGA A 603
4AC4SOFTWAREHIS A:155 , ARG A:162 , TRP A:236 , OGA A:603BINDING SITE FOR RESIDUE GOL A 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:59 -Pro A:60
2Gly A:322 -Pro A:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHX)

(-) 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:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...ee....eee.....eeee.....hhhhhhhhhhhhhh..eeeee...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....eeeee......eeeeeeee.....hhhhh..eeeeee.....eeeeeeee......eeeee......eee.........eeeeeeeee..........................hhhhhhhhhhhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhh...eeee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee....ee......eeeeeeee.....hhhhh..eeeee.....eeeee......eeeeee...eeeee...hhhhhhhhhh......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhx A  24 AEFSDAVTEETLKKQVAEAWSRRTPFSHEVIVMDMDPFLHCVIPNFIQSQDFLEGLQKELMNLDFHEKYNDLYKFQQSDDLKKRREPHISTLRKILFEDFRSWLSDISKIDLESTIDMSCAKYEFTDALLCHDDELEGRRIAFILYLVPPWDRSMGGTLDLYSIDEHFQPKQIVKSLIPSWNKLVFFEVSPVSFHQVSEVLSEEKSRLSISGWFHGPSLTRPPNYFEPPIPRSPHIPQDHEILYDWINPTYLDMDYQVQIQEEFEESSEILLKEFLKPEKFTKVCEALEHGHVEWSSRGPPNKRFYEKAEESKLPEILKECMKLFRSEALFLLLSNFTGLKLHFLAPSSSVPMCQGELRHWKTGHYTLIHAEFALDLILYCGCEGWEPEYGGFTSYIAKGEDEELLTVNPESNSLALVYRDRETLKFVKHINHRSLEQKKTFPNRTGFWDFSFIYYE 542
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       431       441       451|      465       475       485       495       505       515       525       535       
                                                                                                                                                                                                                                                                                                                                                                                     371|                  451|                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                      430                   456
   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 4NHX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  OGFD1_HUMAN | Q8N543
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 Related Entries

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

UniProtKB/Swiss-Prot
        OGFD1_HUMAN | Q8N543: 4nhy

(-) Related Entries Specified in the PDB File

4nhk 4nhl 4nhm 4nhn 4nhy