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(-) Description

Title :  RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A
 
Authors :  S. V. Antonyuk, N. Rustage, R. R. Eady, S. S. Hasnain
Date :  02 Jun 11  (Deposition) - 05 Oct 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Haemoprotein, 4-Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, N. Rustage, C. A. Petersen, J. L. Arnst, D. J. Heyes, R. Sharma, N. G. Berry, N. S. Scrutton, R. R. Eady, C. R. Andrew, S. S. Hasnain
Carbon Monoxide Poisoning Is Prevented By The Energy Costs Of Conformational Changes In Gas- Binding Haemproteins.
Proc. Natl. Acad. Sci. Usa V. 108 15780 2011
PubMed-ID: 21900609  |  Reference-DOI: 10.1073/PNAS.1109051108

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC86
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Synonym: CYTOCHROME C PRIME

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2CMO1Ligand/IonCARBON MONOXIDE
3HEC1Ligand/IonHEME C
4PCA1Mod. Amino AcidPYROGLUTAMIC ACID
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
1ASC2Ligand/IonASCORBIC ACID
2CMO2Ligand/IonCARBON MONOXIDE
3HEC2Ligand/IonHEME C
4PCA2Mod. Amino AcidPYROGLUTAMIC ACID
5SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , LEU A:16 , THR A:17 , MET A:19 , ALA A:20 , TRP A:56 , GLY A:65 , ASP A:67 , ILE A:72 , PHE A:79 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , HIS A:120 , TYR A:123 , ARG A:124 , CMO A:129 , ASC A:130 , SO4 A:131 , HOH A:2032 , HOH A:2248 , HOH A:2250BINDING SITE FOR RESIDUE HEC A 128
2AC2SOFTWARELEU A:16 , MET A:19 , TRP A:56 , HEC A:128BINDING SITE FOR RESIDUE CMO A 129
3AC3SOFTWAREGLY A:113 , HIS A:120 , HEC A:128 , SO4 A:131 , HOH A:2231 , HOH A:2238 , HOH A:2251 , HOH A:2252 , HOH A:2253BINDING SITE FOR RESIDUE ASC A 130
4AC4SOFTWAREARG A:124 , HEC A:128 , ASC A:130 , HOH A:2238 , HOH A:2252BINDING SITE FOR RESIDUE SO4 A 131
5AC5SOFTWAREARG A:69 , LYS A:125 , LYS A:126 , HOH A:2254BINDING SITE FOR RESIDUE SO4 A 132

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  1A:7-125
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  2A:7-125

(-) Exons   (0, 0)

(no "Exon" information available for 2YLD)

(-) Sequences/Alignments

Asymmetric 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:126
 aligned with CYCP_ALCXX | P00138 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           CYCP_ALCXX     1 QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKK 126
               SCOP domains d2ylda_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-125 UniProt: 7-125                                                                                    - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yld A   1 xFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKK 126
                            |       10        20        30        40        50        60        70        80        90       100       110       120      
                            |                                                                                                                             
                            1-PCA
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CYCP_ALCXX | P00138)
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
        CYCP_ALCXX | P00138: 1cgn 1cgo 1e83 1e84 1e85 1e86 2xl6 2xl8 2xld 2xle 2xlh 2xlm 2xlo 2xlv 2xlw 2xm0 2xm4 2ykz 2yl0 2yl1 2yl3 2yl7 2ylg 2yli 3zqv 3zqy 3ztm 3ztz 3zwi 4cda 4cdv 4cdy 4cip 4cjg 4cjo 4d4n 4d4x 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jsl 5jt4 5jua 5jve

(-) Related Entries Specified in the PDB File

1cgn CYTOCHROME C'
1cgo CYTOCHROME C'
1e83 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE
1e84 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE
1e85 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH NO BOUND TO PROXIMAL SIDE OF HEME
1e86 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH CO BOUND TO DISTAL SIDE OF HEME
2xl6 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124A VARIANT WITH BOUND NO
2xl8 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xld CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT
2xle CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT WITH BOUND NO
2xlh REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xlm CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS RECOMBINANT NATIVE WITH BOUND NO
2xlo CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT WITH BOUND NO
2xlv CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124F VARIANT WITH BOUND NO
2xlw CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT WITH BOUND NO
2xm0 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT
2xm4 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT
2ykz RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT
2yl0 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A VARIANT AT 0.95 A RESOLUTION
2yl1 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION
2yl3 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16G VARIANT AT 1.04 A RESOLUTION
2yl7 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G VARIANT AT 0.9 A RESOLUTION
2ylg CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON MONOOXIDE BOUND L16A VARIANT AT 1 .05 A RESOLUTION
2yli RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS IN ITS FERROUS FORM AT 1.45 A