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(-) Description

Title :  STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO-PROTEIN: CU-CUCA-CLOSED
 
Authors :  K. J. Waldron, S. J. Firbank, S. J. Dainty, M. Perez-Rama, S. Tottey, N. J
Date :  20 Jul 10  (Deposition) - 11 Aug 10  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Metal Binding Protein, Cupin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Waldron, S. J. Firbank, S. J. Dainty, M. Perez-Rama, S. Tottey, N. J. Robinson
Structure And Metal Loading Of A Soluble Periplasm Cuproprotein.
J. Biol. Chem. V. 285 32504 2010
PubMed-ID: 20702411  |  Reference-DOI: 10.1074/JBC.M110.153080

(-) Compounds

Molecule 1 - SLL1785 PROTEIN
    Atcc: 27184
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 31-268
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6803
    Organism Taxid: 1148
    Synonym: CUCA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2URE4Ligand/IonUREA
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2URE2Ligand/IonUREA
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2URE2Ligand/IonUREA

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:117 , HIS A:119 , GLU A:124 , HIS A:178 , HOH A:2080 , HOH A:2318BINDING SITE FOR RESIDUE CU A1298
2AC2SOFTWAREGLU A:87 , PRO A:114 , PHE A:214 , PHE A:238 , HOH A:2318 , HOH A:2319BINDING SITE FOR RESIDUE URE A1299
3AC3SOFTWAREHIS B:117 , HIS B:119 , GLU B:124 , HIS B:178 , HOH B:2247BINDING SITE FOR RESIDUE CU B1298
4AC4SOFTWAREGLU B:87 , PRO B:114 , PHE B:214 , PHE B:238 , HOH B:2246 , HOH B:2247BINDING SITE FOR RESIDUE URE B1299
5AC5SOFTWAREHIS C:117 , HIS C:119 , GLU C:124 , HIS C:178 , HOH C:2071 , HOH C:2279BINDING SITE FOR RESIDUE CU C1298
6AC6SOFTWAREGLU C:87 , PRO C:114 , HIS C:117 , PHE C:214 , PHE C:238 , HOH C:2278 , HOH C:2279BINDING SITE FOR RESIDUE URE C1299
7AC7SOFTWAREHIS D:117 , HIS D:119 , GLU D:124 , HIS D:178 , HOH D:2047BINDING SITE FOR RESIDUE CU D1298
8AC8SOFTWAREGLU D:87 , PRO D:114 , HIS D:117 , PHE D:214 , PHE D:238 , HOH D:2047 , HOH D:2228BINDING SITE FOR RESIDUE URE D1299

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:94 -A:296
2B:94 -B:296
3C:94 -C:296
4D:94 -D:296

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XLA)

(-) Exons   (0, 0)

(no "Exon" information available for 2XLA)

(-) 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:233
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:233
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
         P73600_SYNY3    36 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee.....eeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee.......eeeee...hhhhhh..hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xla A  65 HTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 297
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:234
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    
         P73600_SYNY3    35 IHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeee...eeeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee..hhhh.eeeee...hhhhhh..hhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xla B  64 IHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 297
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293    


Chain C from PDB  Type:PROTEIN  Length:235
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:235
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     
         P73600_SYNY3    34 EIHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee...eeeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee.......eeeee...hhhhhh..hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xla C  63 EIHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 297
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     


Chain D from PDB  Type:PROTEIN  Length:234
 aligned with P73600_SYNY3 | P73600 from UniProtKB/TrEMBL  Length:268

    Alignment length:234
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    
         P73600_SYNY3    35 IHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 268
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeee.....eeeeeeeee..eeeeeeeeee........eee..eeeeee......eeeeeeee...............eeeeeee.....eeee...eeeeee......eeeeeeeee............hhhhhhhhhh............hhhhhhhhhhhhhhh.eee.......eeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xla D  64 IHTFDDIPMPKLADPLLIYTPANEIFDIASCSAKDIGFAIAHAQIPPGGGPMPHIHYFINEWFWTPEGGIELFHSTKQYPNMDELPVVGGAGRGDLYSIQSEPKQLIYSPNHYMHGFVNPTDKTLPIVFVWMRNEVAPDFPYHDGGMREYFQAVGPRITDLNNLPELTNAQRAAFASEAPKYGINQSSYFMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNRGDKSVTCS 297
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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  (0, 0)

(no "SCOP Domain" information available for 2XLA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (P73600_SYNY3 | P73600)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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 Related Entries

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

UniProtKB/TrEMBL
        P73600_SYNY3 | P73600: 2xl7 2xl9 2xlf 2xlg

(-) Related Entries Specified in the PDB File

2xl7 STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: CU-CUCA-CLOSED ( SEMET)
2xl9 STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: ZN-CUCA-CLOSED ( SEMET)
2xlf STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: APO-CUCA-CLOSED ( SEMET)
2xlg STRUCTURE AND METAL-LOADING OF A SOLUBLE PERIPLASM CUPRO- PROTEIN: CU-CUCA-OPEN