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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE TESTICULAR CYTOCHROME C AT 1.6 ANGSTROM
 
Authors :  Z. Liu, S. Ye, H. Lin, Z. Rao, X. J. Liu
Date :  01 Aug 05  (Deposition) - 18 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome C, Mouse, Testis, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Liu, H. Lin, S. Ye, Q. Y. Liu, Z. Meng, C. M. Zhang, Y. Xia, E. Margoliash, Z. Rao, X. J. Liu
Remarkably High Activities Of Testicular Cytochrome C In Destroying Reactive Oxygen Species And In Triggering Apoptosis
Proc. Natl. Acad. Sci. Usa V. 103 8965 2006
PubMed-ID: 16757556  |  Reference-DOI: 10.1073/PNAS.0603327103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C, TESTIS-SPECIFIC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBTR1
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:14 , SER A:48 , LYS A:74 , HOH A:304 , HOH A:361 , HOH A:369 , HOH A:477 , HOH A:483BINDING SITE FOR RESIDUE PO4 A 201
2AC2SOFTWARELYS A:54 , ASN A:55 , GLY A:57 , HOH A:339 , HOH A:360 , HOH A:416 , HOH A:446 , HOH A:466 , HOH A:472 , HOH A:506BINDING SITE FOR RESIDUE PO4 A 202
3AC3SOFTWARELYS A:14 , CYS A:15 , GLN A:17 , CYS A:18 , HIS A:19 , THR A:29 , PRO A:31 , THR A:41 , GLY A:42 , TYR A:49 , THR A:50 , ASN A:53 , LYS A:56 , TRP A:60 , TYR A:68 , THR A:79 , LYS A:80 , MET A:81 , ILE A:82 , PHE A:83 , LEU A:99 , HOH A:313BINDING SITE FOR RESIDUE HEM A 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC2_MOUSE2-103  1A:2-103

(-) Exons   (0, 0)

(no "Exon" information available for 2AIU)

(-) 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:104
 aligned with CYC2_MOUSE | P00015 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           CYC2_MOUSE     2 GDAEAGKKIFVQKCAQCHTVEKGGKHKTGPNLWGLFGRKTGQAPGFSYTDANKNKGVIWSEETLMEYLENPKKYIPGTKMIFAGIKKKSEREDLIKYLKQATSS 105
               SCOP domains d2aiua_ A: automated matches                                                                             SCOP domains
               CATH domains 2aiuA00 A:2-105 Cytochrome c                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:2-103 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2aiu A   2 GDAEAGKKIFVQKCAQCHTVEKGGKHKTGPNLWGLFGRKTGQAPGFSYTDANKNKGVIWSEETLMEYLENPKKYIPGTKMIFAGIKKKSEREDLIKYLKQATSS 105
                                    11        21        31        41        51        61        71        81        91       101
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (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 2AIU)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC2_MOUSE | P00015)
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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0042743    hydrogen peroxide metabolic process    The chemical reactions and pathways involving hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0006122    mitochondrial electron transport, ubiquinol to cytochrome c    The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
    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.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
cellular component
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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