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(-) Description

Title :  HEME-PACKING MOTIFS REVEALED BY THE CRYSTAL STRUCTURE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA
 
Authors :  T. M. Iverson, D. M. Arciero, B. T. Hsu, M. S. P. Logan, A. B. Hooper, D. C. Rees
Date :  16 Sep 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome, Electron Transport, Biological Nitrification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Iverson, D. M. Arciero, B. T. Hsu, M. S. Logan, A. B. Hooper, D. C. Rees
Heme Packing Motifs Revealed By The Crystal Structure Of The Tetra-Heme Cytochrome C554 From Nitrosomonas Europaea.
Nat. Struct. Biol. V. 5 1005 1998
PubMed-ID: 9808046  |  Reference-DOI: 10.1038/2975
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C-554
    Chains: A
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 915

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:45 , LYS A:167 , LYS A:193 , HOH A:286BINDING SITE FOR RESIDUE PO4 A 218
2AC2SOFTWARELYS A:39 , LYS A:40 , GLU A:41BINDING SITE FOR RESIDUE PO4 A 219
3AC3SOFTWARELYS A:47 , LEU A:184 , GLU A:185BINDING SITE FOR RESIDUE PO4 A 220
4AC4SOFTWARELYS A:10 , CYS A:11 , CYS A:14 , HIS A:15 , HIS A:92 , HIS A:102 , ARG A:103 , ARG A:118 , GLN A:126 , PHE A:128 , LEU A:184 , GLU A:185 , GLY A:186 , VAL A:187 , LYS A:211 , HEM A:215 , HOH A:222BINDING SITE FOR RESIDUE HEM A 213
5AC5SOFTWARELYS A:39 , ALA A:42 , TYR A:54 , ASP A:59 , CYS A:60 , CYS A:63 , HIS A:64 , CYS A:137 , HIS A:138 , ASN A:140 , PRO A:152 , THR A:154 , PRO A:155 , PHE A:156 , TYR A:164 , HEM A:216 , HOH A:221 , HOH A:275BINDING SITE FOR RESIDUE HEM A 214
6AC6SOFTWARECYS A:11 , SER A:12 , HIS A:15 , GLN A:18 , ALA A:19 , HIS A:27 , GLY A:87 , CYS A:88 , CYS A:91 , HIS A:92 , PHE A:130 , MET A:178 , HIS A:179 , HIS A:181 , TYR A:182 , LEU A:184 , PHE A:194 , HIS A:197 , HEM A:213 , HOH A:222 , HOH A:231 , HOH A:261BINDING SITE FOR RESIDUE HEM A 215
7AC7SOFTWAREALA A:26 , HIS A:27 , ALA A:30 , SER A:33 , LYS A:39 , CYS A:63 , HIS A:64 , VAL A:86 , SER A:90 , ARG A:133 , CYS A:134 , CYS A:137 , HIS A:138 , ALA A:177 , MET A:178 , HEM A:214 , HOH A:262 , HOH A:270BINDING SITE FOR RESIDUE HEM A 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BVB)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:129 -Phe A:130
2Ala A:151 -Pro A:152
3Glu A:191 -Pro A:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BVB)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.C554_NITEU30-167  1A:6-143

(-) Exons   (0, 0)

(no "Exon" information available for 1BVB)

(-) 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:211
 aligned with C554_NITEU | Q57142 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:211
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
           C554_NITEU    25 ADAPFEGRKKCSSCHKAQAQSWKDTAHAKAMESLKPNVKKEAKQKAKLDPAKDYTQDKDCVGCHVDGFGQKGGYTIESPKPMLTGVGCESCHGPGRNFRGDHRKSGQAFEKSGKKTPRKDLAKKGQDFHFEERCSACHLNYEGSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMHEHYKLEGVFEGEPKFKFHDEFQASAKPAKKGK 235
               SCOP domains d1bvba_ A: Cytochrome c554                                                                                                                                                                                          SCOP domains
               CATH domains 1bvbA00 A:1-211 Cytochrome C554; Chain A                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhh.......hhh.....hhhhhh...............hhh.................hhh....hhhhh......hhhhhhhhhhhhhh...eehhhhhh.......hhhhhhhh.......................hhh...hhhhhh..............ee.......hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----MULTIHEME_CYTC  PDB: A:6-143 UniProt: 30-167                                                                                              -------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bvb A   1 ADAPFEGRKKCSSCHKAQAQSWKDTAHAKAMESLKPNVKKEAKQKAKLDPAKDYTQDKDCVGCHVDGFGQKGGYTIESPKPMLTGVGCESCHGPGRNFRGDHRKSGQAFEKSGKKTPRKDLAKKGQDFHFEERCSACHLNYEGSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMHEHYKLEGVFEGEPKFKFHDEFQASAKPAKKGK 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BVB)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C554_NITEU | Q57142)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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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  C554_NITEU | Q57142
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 Related Entries

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

UniProtKB/Swiss-Prot
        C554_NITEU | Q57142: 1ft5 1ft6

(-) Related Entries Specified in the PDB File

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