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(-) Description

Title :  CRYSTAL STRUCTURE OF E51C/E54C PSAZ FROM A.FAECALIS WITH CLANP PROBE
 
Authors :  M. Prudencio, J. Rohovec, J. A. Peters, E. Tocheva, M. J. Boulanger, M. E. Murphy, H. J. Hupkes, W. Kosters, A. Impagliazzo, M. Ubbink
Date :  07 Jul 03  (Deposition) - 07 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Cupredoxin, Nmr Probe, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Prudencio, J. Rohovec, J. A. Peters, E. Tocheva, M. J. Boulanger, M. E. Murphy, H. J. Hupkes, W. Kosters, A. Impagliazzo, M. Ubbink
A Caged Lanthanide Complex As A Paramagnetic Shift Agent For Protein Nmr.
Chemistry V. 10 3252 2004
PubMed-ID: 15224334  |  Reference-DOI: 10.1002/CHEM.200306019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PSEUDOAZURIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24C
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Strain: S-6
    Synonym: CUPREDOXIN, BLUE COPPER PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2Y11Ligand/IonYTTRIUM ION
3YMA1Ligand/Ion7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:40 , CYS A:78 , HIS A:81 , MET A:86BINDING SITE FOR RESIDUE ZN A 124
2AC2SOFTWAREYMA A:195BINDING SITE FOR RESIDUE Y1 A 125
3AC3SOFTWARELYS A:55 , PRO A:108 , LYS A:109 , HOH A:224BINDING SITE FOR RESIDUE SO4 A 126
4AC4SOFTWARECYS A:51 , GLY A:52 , ALA A:53 , CYS A:54 , ASN A:63 , GLU A:113 , GLU A:116 , Y1 A:125 , HOH A:265BINDING SITE FOR RESIDUE YMA A 195

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PY0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:19 -Pro A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PY0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.AZUP_ALCFA95-109  1A:72-86

(-) Exons   (0, 0)

(no "Exon" information available for 1PY0)

(-) 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:122
 aligned with AZUP_ALCFA | P04377 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:122
                                    31        41        51        61        71        81        91       101       111       121       131       141  
           AZUP_ALCFA    22 LAENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPEGAEKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIA 143
               SCOP domains d1py0a_ A: Pseudoazurin                                                                                                    SCOP domains
               CATH domains 1py0A00 A:-1-120 Cupredoxins -  blue copper proteins                                                                       CATH domains
               Pfam domains ------Copper-bind-1py0A01 A:5-93                                                               --------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeee..eeee...eeeeeee.......ee...................eeeee...eeeeee...hhhhh.eeeeee.....hhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------COPPER_BLUE    ---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1py0 A  -1 ASENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPCGACKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIA 120
                                     8        18        28        38        48        58        68        78        88        98       108       118
   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 beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AZUP_ALCFA | P04377)
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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  1py0
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  AZUP_ALCFA | P04377
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 Related Entries

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

UniProtKB/Swiss-Prot
        AZUP_ALCFA | P04377: 1paz 1pza 1pzb 1pzc 2p80 3nyk 3paz 4paz 4rh4 5paz 5x31 6paz 7paz 8paz

(-) Related Entries Specified in the PDB File

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