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(-) Description

Title :  PROTEIN-FOLDING LOCATION CAN REGULATE MN VERSUS CU- OR ZN-BINDING. CRYSTAL STRUCTURE OF MNCA.
 
Authors :  S. Tottey, K. J. Waldron, S. J. Firbank, B. Reale, C. Bessant, K. Sato, J. Gray, M. J. Banfield, C. Dennison, N. J. Robinson
Date :  12 Mar 08  (Deposition) - 28 Oct 08  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Periplasmic Binding Protein, Metal-Binding Protein, Mn2+, Cupin, Bi-Cupin, Oxalate Decarboxylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tottey, K. J. Waldron, S. J. Firbank, B. Reale, C. Bessant, K. Sato, T. R. Cheek, J. Gray, M. J. Banfield, C. Dennison, N. J. Robinson
Protein-Folding Location Can Regulate Manganese-Binding Versus Copper- Or Zinc-Binding.
Nature V. 455 1138 2008
PubMed-ID: 18948958  |  Reference-DOI: 10.1038/NATURE07340

(-) Compounds

Molecule 1 - SLL1358 PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET29A
    Fragment: 35-394
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803
    Synonym: MNCA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2MN6Ligand/IonMANGANESE (II) ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:101 , HIS A:103 , GLU A:108 , HIS A:147 , HOH A:2014BINDING SITE FOR RESIDUE MN A1005
02AC2SOFTWAREHIS A:283 , HIS A:285 , GLU A:290 , HIS A:329 , ACT A:1395BINDING SITE FOR RESIDUE MN A1006
03AC3SOFTWAREHIS B:101 , HIS B:103 , GLU B:108 , HIS B:147 , HOH B:2008BINDING SITE FOR RESIDUE MN B1001
04AC4SOFTWAREHIS B:283 , HIS B:285 , GLU B:290 , HIS B:329 , ACT B:1395BINDING SITE FOR RESIDUE MN B1002
05AC5SOFTWAREHIS C:101 , HIS C:103 , GLU C:108 , HIS C:147 , HOH C:2010BINDING SITE FOR RESIDUE MN C1003
06AC6SOFTWAREHIS C:283 , HIS C:285 , GLU C:290 , HIS C:329 , ACT C:1393BINDING SITE FOR RESIDUE MN C1004
07AC7SOFTWARELEU C:253 , ILE C:272 , ARG C:280 , HIS C:283 , HIS C:285 , GLU C:290 , TYR C:350 , MN C:1004BINDING SITE FOR RESIDUE ACT C1393
08AC8SOFTWAREILE B:272 , ARG B:280 , HIS B:283 , HIS B:285 , GLU B:290 , PHE B:345 , TYR B:350 , MN B:1002BINDING SITE FOR RESIDUE ACT B1395
09AC9SOFTWARELEU A:253 , ILE A:272 , ARG A:280 , HIS A:283 , HIS A:285 , GLU A:290 , TYR A:350 , MN A:1006BINDING SITE FOR RESIDUE ACT A1395
10BC1SOFTWAREVAL B:133 , ASP B:134 , GLY B:137 , ASN B:238BINDING SITE FOR RESIDUE ACT B1396
11BC2SOFTWAREVAL A:133 , ASP A:134 , GLY A:137 , HIS A:237 , ASN A:238BINDING SITE FOR RESIDUE ACT A1396
12BC3SOFTWAREVAL C:133 , ASP C:134 , GLY C:137 , ASN C:238BINDING SITE FOR RESIDUE ACT C1394
13BC4SOFTWARETRP C:47 , GLY C:48 , SER C:311 , VAL C:312BINDING SITE FOR RESIDUE ACT C1395
14BC5SOFTWAREPRO B:94 , GLY B:95 , SER B:211 , GLY B:213 , THR C:195BINDING SITE FOR RESIDUE ACT B1397

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:153 -Pro A:154
2Gly A:213 -Pro A:214
3Gly B:153 -Pro B:154
4Gly B:213 -Pro B:214
5Gly C:153 -Pro C:154
6Gly C:213 -Pro C:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VQA)

(-) 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:356
 aligned with P73510_SYNY3 | P73510 from UniProtKB/TrEMBL  Length:394

    Alignment length:356
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      
         P73510_SYNY3    39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPTQP 394
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eehhhhh..eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee.eeeeeee.....eeeeeee..eeeee....eeeeee.....eeeeeee..........eehhhhhhh.hhhhhhhhhh.hhhhhh........ee.......hhhhh.............eee.......eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee..eeeeee.....eeeeee....eeee....eeeee......eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqa A  39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPTQP 394
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with P73510_SYNY3 | P73510 from UniProtKB/TrEMBL  Length:394

    Alignment length:356
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      
         P73510_SYNY3    39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPTQP 394
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eehhhhh..eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee.eeeeeee.....eeeeeee..eeeee....eeeeee.....eeeeeee.....hhhhheehhhhhhh.hhhhhhhhhh.hhhhhh........ee.......hhhhh.............eee.......eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee..eeeeee.....eeeeee....eeee....eeeee......eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqa B  39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPTQP 394
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      


Chain C from PDB  Type:PROTEIN  Length:354
 aligned with P73510_SYNY3 | P73510 from UniProtKB/TrEMBL  Length:394

    Alignment length:354
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388    
         P73510_SYNY3    39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPT 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC01 C:237-379                                                                                                                      ------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC02 C:237-379                                                                                                                      ------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC03 C:237-379                                                                                                                      ------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC04 C:237-379                                                                                                                      ------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC05 C:237-379                                                                                                                      ------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2vqaC06 C:237-379                                                                                                                      ------------- Pfam domains (6)
         Sec.struct. author ................eehhhhh..eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee.eeeeeee.....eeeeeee..eeeee....eeeeee.....eeeeeee.....hhhhheehhhhhhh.hhhhhhhhhh.hhhhhh........ee.......hhhhh.............eee.......eee..eeeeee...........eeeeeee....eeeeee.....eeeeeee..eeeeee.....eeeeee....eeee....eeeee......eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vqa C  39 WRSLSNVVWGKDLPAFTYAFSKTPLVLYDGGTTKQVGTYNFPVSKGMAGVYMSLEPGAIRELHWHANAAEWAYVMEGRTRITLTSPEGKVEIADVDKGGLWYFPRGWGHSIEGIGPDTAKFLLVFNDGTFSEGATFSVTDWLSHTPIAWVEENLGWTAAQVAQLPKKQVYISSYGPASGPLASATPQGQTAKIEVPHTHNLLGQQPLVSLGGNELRLASAKEFPGSFNMTGALIHLEPGAMRQLHWHPNADEWQYVLDGEMDLTVFASEGKASVSRLQQGDVGYVPKGYGHAIRNSSQKPLDIVVVFNDGDYQSIDLSTWLASNPSSVLGNTFQISPELTKKLPVQDTIFSLPT 392
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   Legend:   → Mismatch (orange background)
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  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 2VQA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (P73510_SYNY3 | P73510)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
    GO:0046564    oxalate decarboxylase activity    Catalysis of the reaction: H(+) + oxalate = CO(2) + formate.
biological process
    GO:0033609    oxalate metabolic process    The chemical reactions and pathways involving oxalate, the organic acid ethanedioate.
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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