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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC CYTOCHROME CB562 ASSEMBLY INDUCED BY NICKEL COORDINATION
 
Authors :  E. N. Salgado, R. A. Lewis, A. L. Rheingold, F. A. Tezcan
Date :  08 Jun 08  (Deposition) - 21 Apr 09  (Release) - 21 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Ni-Stabilized Trimeric Superstructure, Electron Transport, Heme, Iron, Metal-Binding, Periplasm, Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Salgado, R. A. Lewis, S. Mossin, A. L. Rheingold, F. A. Tezcan
Control Of Protein Oligomerization Symmetry By Metal Coordination: C2 And C3 Symmetrical Assemblies Through Cu(Ii) And Ni(Ii) Coordination.
Inorg. Chem. V. 48 2726 2009
PubMed-ID: 19267481  |  Reference-DOI: 10.1021/IC9001237
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:59 , HIS A:63BINDING SITE FOR RESIDUE NI A 107
2AC2SOFTWAREHIS A:73 , HIS A:77BINDING SITE FOR RESIDUE NI A 108
3AC3SOFTWAREALA A:1 , ASP A:39 , LYS A:42BINDING SITE FOR RESIDUE NI A 109
4AC4SOFTWARELEU A:3 , GLU A:4 , MET A:7 , LEU A:14 , PRO A:45 , PRO A:46 , PHE A:61 , GLY A:64 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , HOH A:154BINDING SITE FOR RESIDUE HEM A 150

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DE9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DE9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3de9a_ A: automated matches                                                                               SCOP domains
               CATH domains 3de9A00 A:1-106  [code=1.20.120.10, no name defined]                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3de9 A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMHDFRHGFDILVGQIHDALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
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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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DE9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (C562_ECOLX | P0ABE7)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

2bc5 CRYSTAL STRUCTURE OF E. COLI CYTOCHROME B562 WITH ENGINEERED C-TYPE HEME LINKAGES
2qla CRYSTAL STRUCTURE OF A 16-HELIX BUNDLE ARCHITECTURE PRODUCED BY THE ZINC-MEDIATED SELF ASSEMBLY OF FOUR CYTOCHROME CB562 MOLECULES
3de8 CRYSTAL STRUCTURE OF A DIMERIC CYTOCHROME CB562 ASSEMBLY INDUCED BY COPPER COORDINATION