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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI NRFB
 
Authors :  T. A. Clarke, D. J. Richardson, A. M. Hemmings
Date :  28 Feb 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Pentaheme C-Type Cytochrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Clarke, J. A. Cole, D. J. Richardson, A. M. Hemmings
The Crystal Structure Of The Pentahaem C-Type Cytochrome Nrfb And Characterization Of Its Solution-State Interaction With The Pentahaem Nitrite Reductase Nrfa.
Biochem. J. V. 406 19 2007
PubMed-ID: 17521287  |  Reference-DOI: 10.1042/BJ20070321

(-) Compounds

Molecule 1 - CYTOCHROME C-TYPE PROTEIN NRFB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNRFB6
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 26-188
    Gene: NRFB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1HEC5Ligand/IonHEME C

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:23 , CYS A:24 , CYS A:27 , HIS A:28 , HIS A:57 , PRO A:60 , HIS A:64 , ARG A:65 , GLY A:67 , VAL A:71 , ARG A:73 , HOH A:320 , HOH A:341 , HOH A:357 , HOH A:359BINDING SITE FOR RESIDUE HEC A 201
2AC2SOFTWAREHIS A:28 , GLU A:33 , MET A:35 , HIS A:39 , VAL A:51 , CYS A:53 , CYS A:56 , HIS A:57 , PHE A:74 , HIS A:117 , SER A:118 , LEU A:119 , HIS A:120 , PRO A:121 , HOH A:268 , HOH A:298 , HOH A:311 , HOH A:328 , HOH A:364 , HOH A:375BINDING SITE FOR RESIDUE HEC A 202
3AC3SOFTWARELYS A:29 , LYS A:38 , HIS A:39 , VAL A:42 , ILE A:43 , ASN A:44 , ASN A:55 , CYS A:56 , CYS A:88 , CYS A:91 , HIS A:92 , HIS A:117 , LEU A:119 , GLN A:127 , HEC A:204 , HOH A:247 , HOH A:275 , HOH A:292 , HOH A:338 , HOH A:366BINDING SITE FOR RESIDUE HEC A 203
4AC4SOFTWARECYS A:88 , HIS A:92 , LEU A:97 , ALA A:100 , PHE A:101 , HIS A:104 , CYS A:113 , CYS A:116 , HIS A:117 , ARG A:134 , HEC A:203 , HEC A:205 , HOH A:226 , HOH A:358 , HOH A:361BINDING SITE FOR RESIDUE HEC A 204
5AC5SOFTWARETHR A:54 , ASN A:55 , GLN A:59 , SER A:86 , SER A:90 , PHE A:101 , PRO A:103 , HIS A:107 , LYS A:110 , VAL A:111 , SER A:115 , ILE A:137 , CYS A:138 , CYS A:141 , HIS A:142 , GLN A:145 , HEC A:204 , HOH A:329 , HOH A:356BINDING SITE FOR RESIDUE HEC A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OZY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OZY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OZY)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.NRFB_ECOLI44-172  1A:19-147

(-) Exons   (0, 0)

(no "Exon" information available for 2OZY)

(-) 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:142
 aligned with NRFB_ECOLI | P0ABL1 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:142
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183  
           NRFB_ECOLI    44 NPDAACLDCHKPDTEGMHGKHASVINPNNKLPVTCTNCHGQPSPQHREGVKDVMRFNEPMYKVGEQNSVCMSCHLPEQLQKAFWPHDVHVTKVACASCHSLHPQQDTMQTLSDKGRIKICVDCHSDQRTNPNFNPASVPLLK 185
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhh..........hhhhhhh....hhhhh............hhhhhhhhhh...hhhhhhhhh.hhhhhh...hhhhh.......hhhhhh..hhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MULTIHEME_CYTC  PDB: A:19-147 UniProt: 44-172                                                                                    ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ozy A  19 NPDAACLDCHKPDTEGMHGKHASVINPNNKLPVTCTNCHGQPSPQHREGVKDVMRFNEPMYKVGEQNSVCMSCHLPEQLQKAFWPHDVHVTKVACASCHSLHPQQDTMQTLSDKGRIKICVDCHSDQRTNPNFNPASVPLLK 160
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158
   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 2OZY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OZY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OZY)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NRFB_ECOLI | P0ABL1)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042279    nitrite reductase (cytochrome, ammonia-forming) activity    Catalysis of the reaction: NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+.
biological process
    GO:0019645    anaerobic electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors other than oxygen to generate a transmembrane electrochemical gradient.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    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

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UniProtKB/Swiss-Prot
        NRFB_ECOLI | P0ABL1: 2p0b

(-) Related Entries Specified in the PDB File

2p0b