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(-) Description

Title :  AZURIN DIMER, COVALENTLY CROSSLINKED THROUGH BIS-MALEIMIDOMETHYLETHER
 
Authors :  I. M. C. Van Amsterdam, M. Ubbink, O. Einsle, A. Messerschmidt, A. Merli, D. Cavazzini, G. L. Rossi, G. W. Canters
Date :  30 Aug 01  (Deposition) - 04 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cupredoxin, Electron Transfer, Covalent Crosslink, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. M. C. Van Amsterdam, M. Ubbink, O. Einsle, A. Messerschmidt, A. Merli, D. Cavazzini, G. L. Rossi, G. W. Canters
Dramatic Modulation Of Electron Transfer In Protein Complexes By Crosslinking
Nat. Struct. Biol. V. 9 48 2002
PubMed-ID: 11740504  |  Reference-DOI: 10.1038/NSB736
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AZURIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGK22
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: AZURIN
    Gene: AZU
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2CU2Ligand/IonCOPPER (II) ION
3NI2Ligand/IonNICKEL (II) ION
4OPP1Ligand/Ion1-[PYRROL-1-YL-2,5-DIONE-METHOXYMETHYL]-PYRROLE-2,5-DIONE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:45 , HIS A:46 , CYS A:112 , HIS A:117 , MET A:121BINDING SITE FOR RESIDUE CU A 129
2AC2SOFTWAREGLY B:45 , HIS B:46 , CYS B:112 , HIS B:117 , MET B:121BINDING SITE FOR RESIDUE CU B 129
3AC3SOFTWAREALA A:1 , 144 A:503 , HOH A:553 , HIS B:83BINDING SITE FOR RESIDUE NI A 130
4AC4SOFTWAREHIS A:83 , ALA B:1 , 144 B:504 , HOH B:557BINDING SITE FOR RESIDUE NI B 130
5AC5SOFTWAREALA A:1 , CYS A:3 , NI A:130 , HOH A:513 , HOH A:525 , HOH A:526 , LYS B:74 , ASP B:76 , ASP B:77 , HIS B:83BINDING SITE FOR RESIDUE 144 A 503
6AC6SOFTWARELYS A:74 , ASP A:76 , ASP A:77 , HIS A:83 , ALA B:1 , CYS B:3 , NI B:130 , HOH B:515 , HOH B:527 , HOH B:529 , HOH B:557BINDING SITE FOR RESIDUE 144 B 504
7AC7SOFTWARECYS A:42 , CYS B:42BINDING SITE FOR RESIDUE OPP B 505

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:26
2B:3 -B:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JVL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.AZUR_PSEAE125-141
 		  2A:105-121
B:105-121

(-) Exons   (0, 0)

(no "Exon" information available for 1JVL)

(-) 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:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1jvla_ A: Azurin                                                                                                                SCOP domains
               CATH domains 1jvlA00 A:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee....hhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvl A   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKCVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1jvlb_ B: Azurin                                                                                                                SCOP domains
               CATH domains 1jvlB00 B:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
           Pfam domains (1) Copper-bind-1jvlB01 B:1-128                                                                                                      Pfam domains (1)
           Pfam domains (2) Copper-bind-1jvlB02 B:1-128                                                                                                      Pfam domains (2)
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee....hhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvl B   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKCVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AZUR_PSEAE | P00282)
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.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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  1jvl
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  AZUR_PSEAE | P00282
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 Related Entries

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

UniProtKB/Swiss-Prot
        AZUR_PSEAE | P00282: 1ag0 1azn 1azr 1azu 1bex 1cc3 1e5y 1e5z 1e65 1e67 1etj 1ezl 1gr7 1i53 1ils 1ilu 1jvo 1jze 1jzf 1jzg 1jzh 1jzi 1jzj 1nzr 1r1c 1vlx 1xb3 1xb6 1xb8 2azu 2fnw 2ft6 2ft7 2ft8 2fta 2ghz 2gi0 2hx7 2hx8 2hx9 2hxa 2i7o 2i7s 2idf 2iwe 2oj1 2tsa 2tsb 2xv0 2xv2 2xv3 3azu 3fpy 3fq1 3fq2 3fqy 3fs9 3fsa 3fsv 3fsw 3fsz 3ft0 3ibo 3in0 3in2 3jt2 3jtb 3n2j 3np3 3np4 3oqr 3u25 3uge 4azu 4bww 4hhg 4hhw 4hip 4hz1 4jkn 4k9j 4ko5 4ko6 4ko7 4ko9 4kob 4koc 4mfh 4qkt 4qlw 4wkx 5azu 5i26 5i28

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JVL)