1RUS - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE BINARY COMPLEX OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE AND ITS PRODUCT, 3-PHOSPHO-D-GLYCERATE

Authors :   T. Lundqvist, G. Schneider

Date :   10 Oct 91 (Deposition) - 15 Oct 91 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lyase(Carbon-Carbon) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Lundqvist, G. Schneider
Crystal Structure Of The Binary Complex Of Ribulose-1, 5-Bisphosphate Carboxylase And Its Product, 3-Phospho-D-Glycerate.
J. Biol. Chem. V. 264 3643 1989
PubMed-ID: 2492987
(for further references see the PDB file header)

Molecule 1 - RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)
	Chains	:	A, B
	EC Number	:	4.1.1.39
	Engineered	:	YES
	Organism Scientific	:	RHODOSPIRILLUM RUBRUM
	Organism Taxid	:	1085

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	3PG	2	Ligand/Ion	3-PHOSPHOGLYCERIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:164 , HIS A:287 , ARG A:288 , HIS A:321 , THR A:322 , GLY A:323 , SER A:368 , ASN B:111	BINDING SITE FOR RESIDUE 3PG A 500
2	AC2	SOFTWARE	ASN A:111 , HIS B:287 , ARG B:288 , HIS B:321 , GLY B:323	BINDING SITE FOR RESIDUE 3PG B 500

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:166	-	Pro A:167
2	Lys B:166	-	Pro B:167

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL2_RHORU	186-194	2	A:186-194 B:186-194

(no "Exon" information available for 1RUS)

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:437
 aligned with RBL2_RHORU | P04718 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:455
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452     
           RBL2_RHORU     3 QSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEARELTKIAYPVALFHRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 457
               SCOP domains d1rusa2 A:3-137 Ribulose 1,5-bisphosphate carboxyla          se-oxygenase                                                              d1rusa1 A:138-457 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --1rusA01 A:5-136  [code=3.30.70.150, no name defin          ed]                                                                      1rusA02 A:137-439 Rubisco                                                                                                                                                                                                                                                                                      ------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhhhh..eeeeeeeeee.....hhhhhhhhhhhh....----------......eeeeee...eeeeeeee..............hhhhhhhhh.......eeeeeeeeeee..hhhh..........hhhhhhh.........eeeee........hhhhhhhhhhhh....eee............hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhh.....eeee....hhhh.........hhhhhhhhhhh...eee....--------...hhhhhhhh...................eeeeee......hhhhhhhh.....eeee..........hhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhh.hhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rus A   3 QSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGT----------TRGVDALVYEVDEARELTKIAYPVALFDRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTM--------SSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 457
                                    12        22        32        42        52|        - |      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  |      - |     342       352       362       372       382       392       402       412       422       432       442       452     
                                                                             53         64                                                                                                                                                                                                                                                                  325      334

Chain B from PDB  Type:PROTEIN  Length:435
 aligned with RBL2_RHORU | P04718 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:455
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452     
           RBL2_RHORU     3 QSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEARELTKIAYPVALFHRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 457
               SCOP domains d1rusb2 B:3-137 Ribulose 1,5-bisphosphate carboxyla            se-oxygenase                                                            d1rusb1 B:138-457 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --1rusB01 B:5-136  [code=3.30.70.150, no name defin            ed]                                                                    1rusB02 B:137-439 Rubisco                                                                                                                                                                                                                                                                                      ------------------ CATH domains
           Pfam domains (1) ------RuBisCO_large_N-1rusB03 B:9-134                                                                                               -------RuBisCO_large-1rusB01 B:142-451                                                                                                                                                                                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) ------RuBisCO_large_N-1rusB04 B:9-134                                                                                               -------RuBisCO_large-1rusB02 B:142-451                                                                                                                                                                                                                                                                                       ------ Pfam domains (2)
         Sec.struct. author .....eee...hhhhhhh..eeeeeeeeee.....hhhhhhhhhhhh....------------....eeeeee...eeeeeeee..............hhhhhhhhh.......eeeeeeeeeee..hhhh..........hhhhhhh.........eeeee........hhhhhhhhhhhh....eee............hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhh.....eeee....hhhh.........hhhhhhhhhhh...eee....--------...hhhhhhhh...................eeeeee......hhhhhhhh.....eeee..........hhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhh.hhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rus B   3 QSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGT------------GVDALVYEVDEARELTKIAYPVALFDRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTM--------SSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 457
                                    12        22        32        42        52|        -   |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  |      - |     342       352       362       372       382       392       402       412       422       432       442       452     
                                                                             53           66                                                                                                                                                                                                                                                                325      334

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.150, no name defined] (49)

Rhodospirillum rubrum. Organism_taxid: 1085 (5)

1a	1rusA01	A:5-136
1b	1rusB01	B:5-136

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Rubisco (49)

Rhodospirillum rubrum. Organism_taxid: 1085 (5)

2a	1rusA02	A:137-439
2b	1rusB02	B:137-439

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RuBisCO_large] (36)

Family: RuBisCO_large (36)

Rhodospirillum rubrum (3)

1a	RuBisCO_large-1rusB01	B:142-451
1b	RuBisCO_large-1rusB02	B:142-451

Clan: no clan defined [family: RuBisCO_large_N] (27)

Family: RuBisCO_large_N (27)

Rhodospirillum rubrum (3)

2a	RuBisCO_large_N-1rusB03	B:9-134
2b	RuBisCO_large_N-1rusB04	B:9-134

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RBL2_RHORU | P04718)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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).
	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.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0019253	reductive pentose-phosphate cycle	The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1RUS)

Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

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