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(-) Description

Title :  STRUCTURE OF THE CU(II) FORM OF THE M51A MUTANT OF AMICYANIN
 
Authors :  C. J. Carrell, J. K. Ma, Y. Wang, V. L. Davidson, F. S. Mathews
Date :  21 Jun 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Sandwich, Copper Protein, Electron Transfer, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Ma, Y. Wang, C. J. Carrell, F. S. Mathews, V. L. Davidson
A Single Methionine Residue Dictates The Kinetic Mechanism Of Interprotein Electron Transfer From Methylamine Dehydrogenase To Amicyanin.
Biochemistry V. 46 11137 2007
PubMed-ID: 17824674  |  Reference-DOI: 10.1021/BI7012307
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMICYANIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMEG201
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAUC, AMI
    Mutation: YES
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2MHO1Mod. Amino AcidS-OXYMETHIONINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2QDV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.AMCY_PARDE111-124  1A:85-98

(-) Exons   (0, 0)

(no "Exon" information available for 2QDV)

(-) 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:106
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:106
                                                       54                                                                             
                                                     53 |                                                                             
                                    36        46      | 55        65        75        85        95       105       115       125      
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAK-MKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d2qdva_ A: Amicyanin                                                                                       SCOP domains
               CATH domains 2qdvA00 A:1-105 Cupredoxins--  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee...ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2qdv A   1 DKATIPSESPFAAAEVADGAIVVDIAKmMKYETPELHVKVGDTVTWINREAAPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    10        20       |29        39        49        59        69        79        89        99      
                                                      28-MHO
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMCY_PARDE | P22364)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMCY_PARDE | P22364: 1aac 1aaj 1aan 1bxa 1mda 1mg2 1mg3 1sf3 1sf5 1sfd 1sfh 1t5k 2gb2 2gba 2gc4 2gc7 2idq 2ids 2idt 2idu 2j55 2j56 2j57 2mta 2ov0 2qdw 2rac 3ie9 3iea 3l45 3ply 3rym 4p5r 4p5s

(-) Related Entries Specified in the PDB File

2qdw