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(-) Description

Title :  STRUCTURE OF YCFD, A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COLI IN COMPLEX WITH COBALT AND SUCCINIC ACID.
 
Authors :  N. C. Brissett, A. J. Doherty
Date :  03 Jul 13  (Deposition) - 14 May 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Jmjc Domain, Dioxygenase, Hydroxylation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chowdhury, R. Sekirnik, N. C. Brissett, T. Krojer, C. H. Ho, S. S. Ng, I. J. Clifton, W. Ge, N. J. Kershaw, G. C. Fox, J. R. Muniz, M. Vollmar, C. Phillips, E. S. Pilka, K. L. Kavanagh, F. Von Delft, U. Oppermann, M. A. Mcdonough, A. J. Doherty, C. J. Schofield
Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes To Humans.
Nature V. 509 422 2014
PubMed-ID: 24814345  |  Reference-DOI: 10.1038/NATURE13263

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834S
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B1128, JW1114, YCFD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: RIBOSOMAL OXYGENASE YCFD, ROX

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2SIN1Ligand/IonSUCCINIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SIN2Ligand/IonSUCCINIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , ASP A:161 , HIS A:221 , SIN A:502BINDING SITE FOR RESIDUE CO A 501
2AC2SOFTWAREMET A:146 , SER A:148 , HIS A:159 , ARG A:174 , TRP A:176 , HIS A:221 , ASN A:231 , CO A:501 , HOH A:603 , HOH A:609BINDING SITE FOR RESIDUE SIN A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:100 -Pro A:101
2Glu A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LIV)

(-) Sequences/Alignments

Asymmetric Unit
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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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhh.....eee...........hhhhhhhhhh.....eeeeeee..eeeeee.............eeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee..............eeeee....eeeeee.........eeeeeee....eeee.....eeeee...eeeeeeee...hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............hhhhhhhhhhh...eee.....eeee..eeee..eee...hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4liv A  36 EYQLTLNWPDFLERHWQKRPVVLKRGFNNFIDPISPDELAGLAMESEVDSRLVSHQDGKWQVSHGPFESYDHLGETNWSLLVQAVNHWHEPTAALMRPFRELPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEKLQVDPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNTRELISGFADYVLQRELGGNYYSDPDVPPRAHPADVLPQEMDKLREMMLELINQPEHFKQWFGEFISQSRHELDIAPPEPPYQPDEIYDALKQGEVLVRLGGLRVLRIGDDVYANGEKIDSPHRPALDALASNIALTAENFGDALEDPSFLAMLAALVNSGYWFFEG 407
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175      |197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407
                                                                                                                                                                            182|                                                                                                                                                                                                                    
                                                                                                                                                                             195
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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 4LIV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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  4liv
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  ROXA_ECOLI | P27431
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        ROXA_ECOLI | P27431: 4ccl 4lit 4liu 4nub

(-) Related Entries Specified in the PDB File

4lit SAME PROTEIN IN COMPLEX WITH COBALT AND 2-OXOGLUTARATE
4liu SAME PROTEIN - APO FORM