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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL RUBISCO-LIKE PROTEIN FROM THE GREEN SULFUR BACTERIUM CHLOROBIUM TEPIDUM
 
Authors :  H. Li, M. R. Sawaya, F. R. Tabita, D. Eisenberg
Date :  18 Jan 05  (Deposition) - 17 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrel, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, M. R. Sawaya, F. R. Tabita, D. Eisenberg
Crystal Structure Of A Rubisco-Like Protein From The Green Sulfur Bacterium Chlorobium Tepidum.
Structure V. 13 779 2005
PubMed-ID: 15893668  |  Reference-DOI: 10.1016/J.STR.2005.02.017

(-) Compounds

Molecule 1 - RUBISCO-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-11A
    Expression System Strain: BL-21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CT1772
    Mutation: YES
    Organism Scientific: CHLOROBACULUM TEPIDUM
    Organism Taxid: 1097

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YKW)

(-) Sites  (0, 0)

(no "Site" information available for 1YKW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:172 -Pro A:173
2Lys B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YKW)

(-) Exons   (0, 0)

(no "Exon" information available for 1YKW)

(-) 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:414
 aligned with RBLL_CHLTE | Q8KBL4 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:425
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423     
           RBLL_CHLTE     4 EDVKGFFASRESLDMEQYLVLDYYLESVGDIETALAHFCSEQSTAQWKRVGVDEDFRLVHAAKVIDYEVIEELEQLSYPVKHSETGKIHACRVTIAHPHCNFGPKIPNLLTAVCGEGTYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPNIGLSPGEFAEIAYQSWLGGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDEVDSLMEKHDVAVRNGANALLINALPVGLSAVRMLSNYTQVPLIGHFPFIASFSRMEKYGIHSKVMTKLQRLAGLDAVIMPGFGDRMMTPEEEVLENVIECTKPMGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ 428
               SCOP domains d1ykwa2 A:4-145 Ribulose 1,5-bisphosphate ca           rboxylase-oxygenase                                                                    d1ykwa1 A:146-428 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ykwA01 A:4-145  [code=3.30.70.150, no name            defined]                                                                               1ykwA02 A:146-428 Rubisco                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhh.hhhheeeeeeeeeee.hhhhhhhhhhhh...-----------.......eeeeeeeeeee..............eeeeeeeeeeehhhhh.hhhhhhhhhh.hhhhh.....eeeeeeee.hhhhhh......hhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeee...hhhh......eehhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh........eeeee......hhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykw A   4 EDVKGFFASRESLDMEQYLVLDYYLESVGDIETALAHFCSEQST-----------FRLVHAAKVIDYEVIEELEQLSYPVKHSETGKIHACRVTIAHPHCNFGPKIPNLLTAVCGEGTYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPNIGLSPGEFAEIAYQSWLGGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDEVDSLMEKHDVAVRNGANALLINALPVGLSAVRMLSNYTQVPLIGHFPFIASFSRMEKYGIHSKVMTKLQRLAGLDAVIMPGFGDRVMTPEEEVLENVIECTKPMGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ 428
                                    13        23        33        43   |     -     |  63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423     
                                                                      47          59                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with RBLL_CHLTE | Q8KBL4 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:425
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423     
           RBLL_CHLTE     4 EDVKGFFASRESLDMEQYLVLDYYLESVGDIETALAHFCSEQSTAQWKRVGVDEDFRLVHAAKVIDYEVIEELEQLSYPVKHSETGKIHACRVTIAHPHCNFGPKIPNLLTAVCGEGTYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPNIGLSPGEFAEIAYQSWLGGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDEVDSLMEKHDVAVRNGANALLINALPVGLSAVRMLSNYTQVPLIGHFPFIASFSRMEKYGIHSKVMTKLQRLAGLDAVIMPGFGDRMMTPEEEVLENVIECTKPMGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ 428
               SCOP domains d1ykwb2 B:4-145 Ribulose 1,5-bisphosphate ca           rboxylase-oxygenase                                                                    d1ykwb1 B:146-428 Ribulose 1,  5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ykwB01 B:4-145  [code=3.30.70.150, no name            defined]                                                                               1ykwB02 B:146-428 Rubisco                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------           --------------------------------------------------------------------------------------------RuBisCO_large-1ykwB01 B:  151-428                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) --------------------------------------------           --------------------------------------------------------------------------------------------RuBisCO_large-1ykwB02 B:  151-428                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author .hhhhh..hhhh.hhhheeeeeeeeeee.hhhhhhhhhhhh...-----------.......eeeeeeeeeee..............eeeeeeeeeeehhhhh.hhhhhhhhhh.hhhhh.....eeeeeeee.hhhhhh......hhhhhhhhhhh.....eeeee....--.hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeee...hhhh......eehhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh........eeeee......hhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykw B   4 EDVKGFFASRESLDMEQYLVLDYYLESVGDIETALAHFCSEQST-----------FRLVHAAKVIDYEVIEELEQLSYPVKHSETGKIHACRVTIAHPHCNFGPKIPNLLTAVCGEGTYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPN--LSPGEFAEIAYQSWLGGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDEVDSLMEKHDVAVRNGANALLINALPVGLSAVRMLSNYTQVPLIGHFPFIASFSRMEKYGIHSKVMTKLQRLAGLDAVIMPGFGDRVMTPEEEVLENVIECTKPMGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ 428
                                    13        23        33        43   |     -     |  63        73        83        93       103       113       123       133       143       153       163       173|  |   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423     
                                                                      47          59                                                                                                                174  |                                                                                                                                                                                                                                                           
                                                                                                                                                                                                       177
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RuBisCO_large] (36)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RBLL_CHLTE | Q8KBL4)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016984    ribulose-bisphosphate carboxylase activity    Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
    GO:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).

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    Lys A:172 - Pro A:173   [ RasMol ]  
    Lys B:172 - Pro B:173   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        RBLL_CHLTE | Q8KBL4: 1tel

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