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(-) Description

Title :  DARK OPERATIVE PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (CHLN-CHLB)2 COMPLEX
 
Authors :  M. J. Broecker, S. Schomburg, D. W. Heinz, D. Jahn, W. -D. Schubert, J. Mo
Date :  06 May 10  (Deposition) - 16 Jun 10  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase, Dpor, (Bacterio)Chlorophyll Biosynthesis, Photosynthesis, Nitrogenase-Like (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Broecker, S. Schomburg, D. W. Heinz, D. Jahn, W. -D. Schubert, J. Moser
Crystal Structure Of The Nitrogenase-Like Dark Operative Protochlorophyllide Oxidoreductase Catalytic Complex (Chln/Chlb)2.
J. Biol. Chem. V. 285 27336 2010
PubMed-ID: 20558746  |  Reference-DOI: 10.1074/JBC.M110.126698

(-) Compounds

Molecule 1 - LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
    Chains: A
    EC Number: 1.18.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 146786
    Synonym: LI-POR SUBUNIT N, DPOR SUBUNIT N, CHLN
 
Molecule 2 - LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
    Chains: B
    EC Number: 1.18.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 146786
    Synonym: LI-POR SUBUNIT B, DPOR SUBUNIT B, CHLB

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MGX1Ligand/Ion1-METHYLGUANIDINE
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1MGX2Ligand/Ion1-METHYLGUANIDINE
2SF42Ligand/IonIRON/SULFUR CLUSTER
3SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:22 , CYS A:47 , CYS A:107 , GLY A:138 , ASP B:36BINDING SITE FOR RESIDUE SF4 A 602
2AC2SOFTWAREARG B:257BINDING SITE FOR RESIDUE SO4 B 1503
3AC3SOFTWAREARG B:183 , TYR B:406BINDING SITE FOR RESIDUE SO4 B 1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XDQ)

(-) Sequences/Alignments

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:425
 aligned with CHLN_THEEB | Q8DGH2 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:454
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455    
           CHLN_THEEB     6 PNALNFECETGNYHTFCPISCVAWLYQKIEDSFFLVIGTKTCGYFLQNAMGVMIFAEPRYAMAELEEGDISAQLNDYEELKRLCLEIKRDRNPSVIVWIGTCTTEIIKMDLEGLAPKLEAEIGIPIVVARANGLDYAFTQGEDTVLAAMAARCPTSTAISDPEERNPIQRLLNFGKKKEEVQAQSSQYHPHPPLVLFGSLPDPVVTQLTLELKKQGIKVSGWLPAKRYTELPVIDEGYYVAGVNPFLSRTATTLIRRRKCQLITAPFPIGPDGTRTWIEQICATFGIQPQGLAEREAETWQKLSDYLELVRGKSVFFMGDNLLEISLARFLIRCGMRVLEIGIPYMDKRYQAAELALLSQTCAEMGHPLPTIVEKPDNYNQLQRIKALQPDLVITGMAHANPLEARGISTKWSVEFTFAQIHGFGNARDILELVTRPLRRNQALAGLGWQKLVA 459
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------Oxidored_nitro-2xdqA01 A:22-444                                                                                                                                                                                                                                                                                                                                                                                                        --------------- Pfam domains
         Sec.struct. author ....eeee........hhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhh......-----------------------------.......eeee...hhhhhhhhhhhhhhhh..eeeee...hhhhh.......eeee....hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhh....eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdq A   6 PNALNFECETGNYHTFCPISCVAWLYQKIEDSFFLVIGTKTCGYFLQNAMGVMIFAEPRYAMAELEEGDISAQLNDYEELKRLCLEIKRDRNPSVIVWIGTCTTEIIKMDLEGLAPKLEAEIGIPIVVARANGLDYAFTQGEDTVLAAMAARCPTST-----------------------------QYHPHPPLVLFGSLPDPVVTQLTLELKKQGIKVSGWLPAKRYTELPVIDEGYYVAGVNPFLSRTATTLIRRRKCQLITAPFPIGPDGTRTWIEQICATFGIQPQGLAEREAETWQKLSDYLELVRGKSVFFMGDNLLEISLARFLIRCGMRVLEIGIPYMDKRYQAAELALLSQTCAEMGHPLPTIVEKPDNYNQLQRIKALQPDLVITGMAHANPLEARGISTKWSVEFTFAQIHGFGNARDILELVTRPLRRNQALAGLGWQKLVA 459
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155      |  -         -         -      |195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455    
                                                                                                                                                                                      162                           192                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:440
 aligned with CHLB_THEEB | Q8DGC6 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:440
                                    10        20        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
           CHLB_THEEB     1 MKLAYWMYAGPAHIGTLRIASSFKNVHGIMHAPLGDDYFNVMRSMLERERDFTPVTASIVDRHVLARGSQEKVVDNIIRKDTEEHPDLIVLTPTCTSSILQEDLQNFVRRASLSTTADVLLADVNHYRVNELQAADRTLEQIVQFYIDKARRQGTLGTSKTPTPSVNIIGITTLGFHNQHDCRELKQLMADLGIQVNLVIPAAATVHDLQRLPQAWFNLVPYREIGGLTAQYLEREFGQPSVRITPMGVVETARCIRAIQGVLNAQGAGVNYEAFIEQQTREVSQAAWFSRSIDCQNLTGKKAVVFGDNTHAAAMTKILSREMGIHVVWAGTYCKYDADWFRAEVAGFCDEVLITDDHTVVGDAIARVEPAAIFGTQMERHVGKRLNIPCGVIAAPIHIQDFPVGYRPFLGYEGTNQLVDLIYNSFTLGMEDHLLEIFGG 440
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Oxidored_nitro-2xdqB01 B:11-427                                                                                                                                                                                                                                                                                                                                                                                                  ------------- Pfam domains
         Sec.struct. author .eee......hhhhhhhhhhh....eeeeeee....hhhhhhhhhhh.......eeeee...........hhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.....hhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhh.eee......hhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhhhh..eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdq B   1 MKLAYWMYAGPAHIGTLRIASSFKNVHGIMHAPLGDDYFNVMRSMLERERDFTPVTASIVDRHVLARGSQEKVVDNIIRKDTEEHPDLIVLTPTCTSSILQEDLQNFVRRASLSTTADVLLADVNHYRVNELQAADRTLEQIVQFYIDKARRQGTLGTSKTPTPSVNIIGITTLGFHNQHDCRELKQLMADLGIQVNLVIPAAATVHDLQRLPQAWFNLVPYREIGGLTAQYLEREFGQPSVRITPMGVVETARCIRAIQGVLNAQGAGVNYEAFIEQQTREVSQAAWFSRSIDCQNLTGKKAVVFGDNTHAAAMTKILSREMGIHVVWAGTYCKYDADWFRAEVAGFCDEVLITDDHTVVGDAIARVEPAAIFGTQMERHVGKRLNIPCGVIAAPIHIQDFPVGYRPFLGYEGTNQLVDLIYNSFTLGMEDHLLEIFGG 440
                                    10        20        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
   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 2XDQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Oxidored_nitro] (12)

(-) Gene Ontology  (14, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHLN_THEEB | Q8DGH2)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016730    oxidoreductase activity, acting on iron-sulfur proteins as donors    Catalysis of an oxidation-reduction (redox) reaction in which an iron-sulfur protein acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0016636    oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces an iron-sulfur protein.
biological process
    GO:0015995    chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.
    GO:0036068    light-independent chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors, which occur in the absence of light.
    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:0019685    photosynthesis, dark reaction    A complex cycle of enzyme-mediated reactions which catalyzes the reduction of carbon dioxide to sugar. As well as carbon dioxide the cycle requires reducing power in the form of reduced nicotinamide adenine dinucleotide phosphate (NADP) and chemical energy in the form of adenosine triphosphate (ATP). The reduced NADP (NADPH) and ATP are produced by the 'light' reactions.

Chain B   (CHLB_THEEB | Q8DGC6)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016730    oxidoreductase activity, acting on iron-sulfur proteins as donors    Catalysis of an oxidation-reduction (redox) reaction in which an iron-sulfur protein acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0016636    oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces an iron-sulfur protein.
biological process
    GO:0015995    chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.
    GO:0036068    light-independent chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors, which occur in the absence of light.
    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:0019685    photosynthesis, dark reaction    A complex cycle of enzyme-mediated reactions which catalyzes the reduction of carbon dioxide to sugar. As well as carbon dioxide the cycle requires reducing power in the form of reduced nicotinamide adenine dinucleotide phosphate (NADP) and chemical energy in the form of adenosine triphosphate (ATP). The reduced NADP (NADPH) and ATP are produced by the 'light' reactions.
    GO:0046148    pigment biosynthetic process    The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms, e.g. melanin.

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  CHLB_THEEB | Q8DGC6
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  CHLN_THEEB | Q8DGH2
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 Related Entries

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