3AXK - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF RICE RUBISCO IN COMPLEX WITH NADP(H)

Authors :   H. Matsumura, E. Mizohata, H. Ishida, A. Kogami, T. Ueno, A. Makino, T. I A. Yokota, T. Mae, Y. Kai

Date :   11 Apr 11 (Deposition) - 11 Apr 12 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,S,T
Biol. Unit 1: A,B,S,T  (4x)

Keywords :   Alpha/Beta Barrel, Photosynthetic Carbon Reduction, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Matsumura, E. Mizohata, H. Ishida, A. Kogami, T. Ueno, A. Makino, T. Inoue, A. Yokota, T. Mae, Y. Kai
Crystal Structure Of Rice Rubisco And Implications For Activation Induced By Positive Effectors Nadph And 6-Phosphogluconate
J. Mol. Biol. V. 422 75 2012
PubMed-ID: 22609438 | Reference-DOI: 10.1016/J.JMB.2012.05.014

Molecule 1 - RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
	Chains	:	A, B
	EC Number	:	4.1.1.39
	Organism Common	:	JAPANESE RICE
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Synonym	:	RUBISCO LARGE SUBUNIT, D-RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE SUBUNIT
	Tissue	:	LEAVES

Molecule 2 - RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN, CHLOROPLASTIC
	Chains	:	S, T
	EC Number	:	4.1.1.39
	Organism Common	:	JAPANESE RICE
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Synonym	:	RUBISCO SMALL SUBUNIT, D-RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE SMALL SUBUNIT
	Tissue	:	LEAVES

		1	2	3	4
Asymmetric Unit	:	A	B	S	T
Biological Unit 1 (4x)	:	A	B	S	T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 12)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5	NME	2	Mod. Amino Acid	METHYLAMINE

Biological Unit 1 (4, 40)

No.	Name	Count	Type	Full Name
1	GOL	16	Ligand/Ion	GLYCEROL
2	KCX	8	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NDP	8	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5	NME	8	Mod. Amino Acid	METHYLAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:270 , GLY A:273 , MET A:297 , ILE A:301 , HOH A:627 , HOH A:628 , HOH A:629 , LEU B:270 , ILE B:301	BINDING SITE FOR RESIDUE GOL A 501
2	AC2	SOFTWARE	HIS A:86 , GLU A:88 , LYS A:356 , ARG A:358 , HOH B:976	BINDING SITE FOR RESIDUE GOL A 502
3	AC3	SOFTWARE	KCX A:201 , ASP A:203 , GLU A:204 , HOH A:616 , HOH A:693 , HOH A:901	BINDING SITE FOR RESIDUE MG A 478
4	AC4	SOFTWARE	LYS A:175 , HIS A:294 , ARG A:295 , HIS A:298 , SER A:379 , GLY A:380 , GLY A:381 , GLY A:403 , GLY A:404 , GLY A:405 , HOH A:580 , HOH A:595 , HOH A:614 , HOH A:616 , HOH A:693 , HOH A:758 , HOH A:1073 , HOH A:1080 , HOH A:1081 , HOH A:1083 , HOH A:1085 , HOH A:1086 , HOH A:1115 , GLU B:60 , ASN B:123 , GLY B:126 , PHE B:127 , HOH B:733	BINDING SITE FOR RESIDUE NDP A 479
5	AC5	SOFTWARE	GLU A:60 , THR A:68 , ASN A:123 , GLY A:126 , PHE A:127 , HOH A:534 , HOH A:594 , HOH A:854 , HOH A:1074 , HOH A:1076 , HOH A:1090 , HOH A:1091 , HOH A:1092 , HOH A:1093 , HOH A:1096 , LYS B:175 , HIS B:294 , ARG B:295 , HIS B:298 , SER B:379 , GLY B:380 , GLY B:381 , ILE B:382 , GLY B:404 , GLY B:405 , HOH B:696 , HOH B:787 , HOH B:855 , HOH B:1078 , HOH B:1079 , HOH B:1087 , HOH B:1125	BINDING SITE FOR RESIDUE NDP A 480
6	AC6	SOFTWARE	SER A:145 , LYS A:146 , PHE A:148 , ARG A:213 , HOH A:497 , HOH A:539 , HOH A:1109 , GLU B:110 , GOL B:504	BINDING SITE FOR RESIDUE GOL B 503
7	AC7	SOFTWARE	LYS A:146 , THR A:147 , HOH A:894 , HOH A:895 , GOL B:503 , HOH B:654	BINDING SITE FOR RESIDUE GOL B 504
8	AC8	SOFTWARE	KCX B:201 , ASP B:203 , GLU B:204 , HOH B:734 , HOH B:787 , HOH B:855	BINDING SITE FOR RESIDUE MG B 478

Asymmetric Unit

No.	Residues
1	A:247	-	B:247

Asymmetric Unit

No.	Residues
1	Lys A:175	-	Pro A:176
2	Lys B:175	-	Pro B:176

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

Asymmetric 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.	RBL_ORYSJ	196-204	2	A:196-204 B:196-204

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL_ORYSJ	196-204	8	A:196-204 B:196-204

(no "Exon" information available for 3AXK)

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:434
 aligned with RBL_ORYSJ | P0C512 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:443
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459   
            RBL_ORYSJ    20 YKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMRWRDRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRARGIFFTQDWVSMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIW 462
               SCOP domains d3axka1 A:20-150 Ribulose 1,5-bisphosphate c    arboxylase-oxygenase                                                               d3axka2 A:151-462 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh..----.hhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eeeee...-----hhhhhhhhhhhhhh.ee..hhhhh....ee.......eeeee...hhhhhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3axk A  20 YKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESST----TVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTkDDENVNSQPFMRWRDRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVV-----EREMTLGFVDLLRDDFIEKDRARGIFFTQDWVSMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIW 462
                                    29        39        49        59   |    69        79        89        99       109       119       129       139       149       159       169       179       189       199 |     209       219       229       239       249       259       269       279       289       299       309       319       329  |    339       349       359       369       379       389       399       409       419       429       439       449       459   
                                                                      63   68                                                                                                                                  201-KCX                                                                                                                            332   338

Chain B from PDB  Type:PROTEIN  Length:430
 aligned with RBL_ORYSJ | P0C512 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:443
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460   
            RBL_ORYSJ    21 KLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMRWRDRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRARGIFFTQDWVSMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIWK 463
               SCOP domains d3axkb1 B:21-150 Ribulose 1,5-bisphosphate       carboxylase-oxygenase                                                            d3axkb2 B:151-463 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee....hhhhhhhhhhhhh..------hhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eeeee.-------hhhhhhhhhhhhhh.ee..hhhhh....ee.......eeeee...hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3axk B  21 KLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESST------WTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTkDDENVNSQPFMRWRDRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGT-------EREMTLGFVDLLRDDFIEKDRARGIFFTQDWVSMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRSACKWSPELAAACEIWK 463
                                    30        40        50        60  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460   
                                                                     63     70                                                                                                                                201-KCX                                                                                                                          330     338

Chain S from PDB  Type:PROTEIN  Length:121
 aligned with RBS1_ORYSJ | Q0INY7 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:121
                                    56        66        76        86        96       106       116       126       136       146       156       166 
           RBS1_ORYSJ    47 CMQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPP 167
               SCOP domains d3axks_ S: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhh..eeeeeee.....................eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3axk S   0 xMQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQCISFIAYKPP 121
                            |        9        19        29        39      ||50        60        70        80        90       100       110       120 
                            0-NME                                        46|                                                                         
                                                                          48

Chain T from PDB  Type:PROTEIN  Length:120
 aligned with RBS1_ORYSJ | Q0INY7 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:120
                                    56        66        76        86        96       106       116       126       136       146       156       166
           RBS1_ORYSJ    47 CMQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKP 166
               SCOP domains d3axkt_ T: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhh..eeeeeee.....................eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3axk T   0 xMQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQCISFIAYKP 120
                            |        9        19        29        39      ||50        60        70        80        90       100       110       120
                            0-NME                                        46|                                                                        
                                                                          48

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 '\|'

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

(no "Pfam Domain" information available for 3AXK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RBL_ORYSJ | P0C512)

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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0009853	photorespiration	A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
	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.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Chain S,T (RBS1_ORYSJ | Q0INY7)

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: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:0009853	photorespiration	A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
	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.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:175 - Pro A:176	[ RasMol ]
		Lys B:175 - Pro B:176	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3axk
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	RBS1_ORYSJ \| Q0INY7
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	4.1.1.39
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		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/Swiss-Prot
	RBL_ORYSJ \| P0C512	:	1wdd 3axm
	RBS1_ORYSJ \| Q0INY7	:	1wdd 3axm

1wdd	STRUCTURE OF RICE RUBISCO IN COMPLEX WITH CABP
3axm	STRUCTURE OF RICE RUBISCO IN COMPLEX WITH 6PG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (8, 8)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 25)

Visualization

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Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File