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(-) Description

Title :  CRYSTAL STRUCTURE OF RUBISCO-LIKE PROTEIN FROM RHODOPSEUDOMONAS PALUSTRIS
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. A. Gerlt, S. K. Burley, S. C. Almo, New Yo Research Center For Structural Genomics (Nysgxrc)
Date :  23 Jan 11  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Rlp Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. A. Gerlt, S. K. Burley, S. C. Almo
Crystal Structure Of Rubisco-Like Protein From Rhodopseudomonas Palustris
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE SUBUNIT
    Chains: A, B
    EC Number: 4.1.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPC_2184
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 316056
    Strain: BISB18
    Synonym: RUBISCO-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:328 , ARG A:332 , HOH A:457 , ASN B:312 , HOH B:394BINDING SITE FOR RESIDUE SO4 A 379
2AC2SOFTWARESER A:293 , THR A:294 , GLN B:129BINDING SITE FOR RESIDUE SO4 A 380
3AC3SOFTWAREGLY A:127 , GLN A:129 , SER A:130 , ARG A:131BINDING SITE FOR RESIDUE SO4 A 381
4AC4SOFTWAREGLN A:129 , SER B:293 , THR B:294 , HOH B:477BINDING SITE FOR RESIDUE SO4 B 379
5AC5SOFTWAREASN B:328 , ARG B:332 , HOH B:438BINDING SITE FOR RESIDUE SO4 B 380
6AC6SOFTWAREGLY B:127 , GLN B:129 , SER B:130 , ARG B:131BINDING SITE FOR RESIDUE SO4 B 381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QFW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:139 -Pro A:140
2Lys B:139 -Pro B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QFW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QFW)

(-) Exons   (0, 0)

(no "Exon" information available for 3QFW)

(-) 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:347
 aligned with Q216E8_RHOPB | Q216E8 from UniProtKB/TrEMBL  Length:368

    Alignment length:368
                                                                                                                                                                                                                                                                                                                                                                                                        368 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      | 
         Q216E8_RHOPB     2 TEPRIVATYHIASDAERIEQRALALAIEQSVECPLEAIGDPAIVANIVGRVEDVAELQPGRYAVRIGLAAATAPAEPGQLLNMLFGNSSIQPDIALADVELPAHYLTAFGGPRVGLAGIRTLTGAQSRALTASALKPQGLSPAALASIAHQLALGGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISGTLDDMRRQLGVIRDEGIGAVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAAKIAAPLLLGRLFRLFGADATVFPNYGGRFAYSTASCLALAQAARDPFGKLNACIPTPAGGIMLQRVNELLRFYGQDVMLLIGGSLLASRERLTEQASRFVNKVADYGQR-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.hhhhhhhhhhhhhhhh....hhhhh-------....eeeeeeeee..eeeeeeeehhhhh..hhhhhhhhhhhhhhhh..ee...ee.hhhhhhhhh...hhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.....eeee.....---..hhhhhhhhhhhhhh..eeeee...--...hhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eee.---------hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfw A   4 TEPRIVATYHIASDAERIEQRALALAIEQSVECPLEAI-------NIVGRVEDVAELQPGRYAVRIGLAAATAPAEPGQLLNMLFGNSSIQPDIALADVELPAHYLTAFGGPRVGLAGIRTLTGAQSRALTASALKPQGLSPAALASIAHQLALGGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISGTLDDMRRQLGVIRDEGIGAVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMA---KIAAPLLLGRLFRLFGADATVFPNYG--FAYSTASCLALAQAARDPFGKLNACIPTPAGGIMLQRVNELLRFYGQDVMLLI---------RLTEQASRFVNKVADYGQRE 371
                                    13        23        33       | -     |  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        |-       353       363        
                                                                41      49                                                                                                                                                                                                              258 262                      287  |                                                 342       352                   
                                                                                                                                                                                                                                                                                                                        290                                                                                 


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q216E8_RHOPB | Q216E8 from UniProtKB/TrEMBL  Length:368

    Alignment length:368
                                                                                                                                                                                                                                                                                                                                                                                                        368 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      | 
         Q216E8_RHOPB     2 TEPRIVATYHIASDAERIEQRALALAIEQSVECPLEAIGDPAIVANIVGRVEDVAELQPGRYAVRIGLAAATAPAEPGQLLNMLFGNSSIQPDIALADVELPAHYLTAFGGPRVGLAGIRTLTGAQSRALTASALKPQGLSPAALASIAHQLALGGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISGTLDDMRRQLGVIRDEGIGAVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAAKIAAPLLLGRLFRLFGADATVFPNYGGRFAYSTASCLALAQAARDPFGKLNACIPTPAGGIMLQRVNELLRFYGQDVMLLIGGSLLASRERLTEQASRFVNKVADYGQR-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------RuBisCO_large-3qfwB01 B:118-282                                                                                                                                      ----------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------RuBisCO_large-3qfwB02 B:118-282                                                                                                                                      ----------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eee..eee.hhhhhhhhhhhhhhhh....hhhhh-------....eeeeeeeee..eeeeeeeehhhhh..hhhhhhhhhhhhhhhh..ee...ee.hhhhhhhhh...hhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh........eeeee......hhhhhhhhhh...eee.---------hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfw B   4 TEPRIVATYHIASDAERIEQRALALAIEQSVECPLEAI-------NIVGRVEDVAELQPGRYAVRIGLAAATAPAEPGQLLNMLFGNSSIQPDIALADVELPAHYLTAFGGPRVGLAGIRTLTGAQSRALTASALKPQGLSPAALASIAHQLALGGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISGTLDDMRRQLGVIRDEGIGAVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAAKIAAPLLLGRLFRLFGADATVFPNYGGRFAYSTASCLALAQAARDPFGKLNACIPTPAGGIMLQRVNELLRFYGQDVMLLI---------RLTEQASRFVNKVADYGQRE 371
                                    13        23        33       | -     |  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        |-       353       363        
                                                                41      49                                                                                                                                                                                                                                                                                                  342       352
   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  (0, 0)

(no "SCOP Domain" information available for 3QFW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QFW)

(-) 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   (Q216E8_RHOPB | Q216E8)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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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