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(-) Description

Title :  CRYSTAL STRUCTURE OF DPH2 FROM PYROCOCCUS HORIKOSHII
 
Authors :  Y. Zhang, X. Zhu, A. T. Torelli, M. Lee, B. Dzikovski, R. M. Koralewski, E J. Freed, C. Krebs, H. Lin, S. E. Ealick
Date :  01 Mar 10  (Deposition) - 23 Jun 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Diphthamide Biosynthesis, Radical Sam Enzyme, Gene Triplication, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, X. Zhu, A. T. Torelli, M. Lee, B. Dzikovski, R. M. Koralewski, E. Wang, J. Freed, C. Krebs, S. E. Ealick, H. Lin
Diphthamide Biosynthesis Requires An Organic Radical Generated By An Iron-Sulphur Enzyme.
Nature V. 465 891 2010
PubMed-ID: 20559380  |  Reference-DOI: 10.1038/NATURE09138

(-) Compounds

Molecule 1 - DPH2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDESTF1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3LZC)

(-) Sites  (0, 0)

(no "Site" information available for 3LZC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LZC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LZC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LZC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LZC)

(-) Exons   (0, 0)

(no "Exon" information available for 3LZC)

(-) 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:342
 aligned with DPH2_PYRHO | O58832 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
           DPH2_PYRHO     1 MLHEIPKSEILKELKRIGAKRVLIQSPEGLRREAEELAGFLEENNIEVFLHGEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVSVVEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLESEGFEVSIGRGDSRISWPGQVLGCNYSVAKVRGEGILFIGSGIFHPLGLAVATRKKVLAIDPYTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQLRLAEAKRIVKLLKKHGREARLIVMNDVNYHKLEGFPFEAYVVVACPRVPLDDYGAWRKPVLTPKEVEILLGLREEYEFDEILGGPRESDEPFGISIHSTR 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhh...eeeeee...........eeeee......hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..eee..................hhhhh....eeeee...hhhhhhhhhhhh.eeeee......eee..hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhh..eeeeeee...hhhhhh.....eeee...hhhhhh........eehhhhhhhhh........................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lzc A   1 MLHEIPKSEILKELKRIGAKRVLIQSPEGLRREAEELAGFLEENNIEVFLHGEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVSVVEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLESEGFEVSIGRGDSRISWPGQVLGCNYSVAKVRGEGILFIGSGIFHPLGLAVATRKKVLAIDPYTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQLRLAEAKRIVKLLKKHGREARLIVMNDVNYHKLEGFPFEAYVVVACPRVPLDDYGAWRKPVLTPKEVEILLGLREEYEFDEILGGPRESDEPFGISIHSTR 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with DPH2_PYRHO | O58832 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           DPH2_PYRHO     1 MLHEIPKSEILKELKRIGAKRVLIQSPEGLRREAEELAGFLEENNIEVFLHGEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVSVVEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLESEGFEVSIGRGDSRISWPGQVLGCNYSVAKVRGEGILFIGSGIFHPLGLAVATRKKVLAIDPYTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQLRLAEAKRIVKLLKKHGREARLIVMNDVNYHKLEGFPFEAYVVVACPRVPLDDYGAWRKPVLTPKEVEILLGLREEYEFDEILGGPRESDEPFGISIHST 341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhh...eeeeee...........eeeee.....hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..eee..................hhhhh.....eeee...hhhhhhhhhhhh..eeee......eee..hhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh..eeeeeee...hhhhhh.....eeee...hhhhhh--......eehhhhhhhhh........................eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzc B   1 MLHEIPKSEILKELKRIGAKRVLIQSPEGLRREAEELAGFLEENNIEVFLHGEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVSVVEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLESEGFEVSIGRGDSRISWPGQVLGCNYSVAKVRGEGILFIGSGIFHPLGLAVATRKKVLAIDPYTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQLRLAEAKRIVKLLKKHGREARLIVMNDVNYHKLEGFPFEAYVVVACPRVPLD--GAWRKPVLTPKEVEILLGLREEYEFDEILGGPRESDEPFGISIHST 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  |  | 300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                              293  |                                             
                                                                                                                                                                                                                                                                                                                                 296
   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 3LZC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LZC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LZC)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPH2_PYRHO | O58832)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0050843    S-adenosylmethionine catabolic process    The chemical reactions and pathways resulting in the breakdown of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
    GO:0017183    peptidyl-diphthamide biosynthetic process from peptidyl-histidine    The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPH2_PYRHO | O58832: 3lzd

(-) Related Entries Specified in the PDB File

3lzd DIPHTHAMIDE BIOSYNTHESIS REQUIRES A SAM-DEPENDANT [4FE-4S]- CONTAINING ENZYME