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(-) Description

Title :  CYSTEINE DIOXYGENASE VARIANT - Y157F AT PH 8.0 IN COMPLEX WITH HOMOCYSTEINE
 
Authors :  C. M. Driggers, P. A. Karplus
Date :  26 Dec 14  (Deposition) - 24 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Cupin Fold, Cysteine To Cysteine Sulfinic Acid Catalysis, Thiol Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Driggers, L. L. Hischberger, M. H. Stipanuk, P. A. Karplus
Structures Of Mammalian Cysteine Dioxygenase Variants Missing The Cys-Tyr Crosslink
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYSTEINE DIOXYGENASE TYPE 1
    Chains: A
    EC Number: 1.13.11.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDO1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: CYSTEINE DIOXYGENASE TYPE I,CDO-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:140 , HCS A:502binding site for residue FE A 501
2AC2SOFTWARETYR A:58 , ARG A:60 , HIS A:86 , HIS A:88 , CYS A:93 , HIS A:140 , HIS A:155 , PHE A:157 , MET A:179 , FE A:501 , HOH A:717binding site for residue HCS A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XFA)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhh.......eeeeee......eeeeeee.......ee.....eeeeeeee..eeeeee.............eeeee....eeee.....eeeee.......eeeeeeee....eeeee......eeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xfa A   5 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLFSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP 190
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4XFA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xfa
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  CDO1_RAT | P21816
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  1.13.11.20
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDO1_RAT | P21816: 2b5h 2gh2 3eln 4ieo 4iep 4ieq 4ier 4ies 4iet 4ieu 4iev 4iew 4iex 4iey 4iez 4jtn 4jto 4kwj 4kwk 4kwl 4pix 4piy 4piz 4pjy 4ubg 4ubh 4xet 4xez 4xf0 4xf1 4xf3 4xf4 4xf9 4xfb 4xfc 4xff 4xfg 4xfh 4xfi 4yni 4ysf 4yyo 4z82 5efu 5ezw 5fdb 5i0r 5i0s 5i0t 5i0u

(-) Related Entries Specified in the PDB File

4ext FE-CL BOUND Y157F AT PH ~7.0 IN THE PRESENCE OF AZIDE
4ieo UNLIGANDED WT CDO AT PH 4.0 IN THE PRESENCE OF CYS
4iep UNLIGANDED WT CDO AT PH 4.5 IN THE PRESENCE OF CYS
4ieq UNLIGANDED WT CDO AT PH 5.0 IN THE PRESENCE OF CYS
4ier CYS-PERSULFENATE BOUND WT CDO AT PH 5.5 IN THE PRESENCE OF CYS
4ies CYS-PERSULFEANTE BOUND WT CDO AT PH 6.2 IN THE PRESENCE OF CYS
4iet CYS-PERSULFEANTE BOUND WT CDO AT PH 6.8 IN THE PRESENCE OF CYS
4ieu CYS-PERSULFENATE BOUND WT CDO AT PH 7.0 IN THE PRESENCE OF CYS
4iev CYS-ONLY BOUND WT CDO AT PH 8.0 IN THE PRESENCE OF CYS
4iew CYS-ONLY BOUND CYSTEINE DIOXYGENASE AT PH 9.0 IN THE PRESENCE OF CYS
4iex UNLIGANDED ROOM-TEMP WT CDO AT PH 6.2
4iey CYS-PERSULFEANTE BOUND WT CDO AT PH 7.0 IN THE PRESENCE OF CYS,HOME- SOURCE STRUCTURE
4iez UNLIGANDED WT CDO AT PH 8.0
4jtn WT CDO AT PH 8.0 IN THE PRESENCE OF DITHIONITE
4jto CYS-ONLY BOUND WT CDO AT PH 8.0 IN THE PRESENCE OF CYS AND DITHIONITE
4kwk CYS-PERSULFIDE BOUND WT CDO
4kwl 3-MERCAPTOPROPIONATE-PERSULFIDE BOUND WT CDO
4pix UNLIGANDED C93A CDO AT PH 6.2
4piy HOMOCYSTEINE-BOUND C93A CDO AT PH 6.2
4piz HOMOCYSTEINE-BOUND WT CDO AT PH 6.2
4pjy AZIDE-BOUND WT CDO AT PH 6.2
4xez CYSTEINE DIOXYGENASE VARIANT - Y157F AT PH 8.0 WITH DITHIONITE
4xf0 CYSTEINE DIOXYGENASE VARIANT - C93A AT PH 8.0 WITH CYSTEINE
4xf1 CYSTEINE DIOXYGENASE VARIANT - Y157F AT PH 8.0 WITH CYSTEINE
4xf3 CYSTEINE DIOXYGENASE VARIANT - Y157F AT PH 8.0 WITH CYSTEINE AND DITHIONITE
4xf4 CYSTEINE DIOXYGENASE AT PH 8.0 IN COMPLEX WITH HOMOCYSTEINE
4xf9 CYSTEINE DIOXYGENASE VARIANT - C93A AT PH 8.0 IN COMPLEX WITH HOMOCYSTEINE
4xfb
4xfc
4xff
4xfg
4xfh
4xfi