1KTP - JenaLib

Title :   CRYSTAL STRUCTURE OF C-PHYCOCYANIN OF SYNECHOCOCCUS VULCANUS AT 1.6 ANGSTROMS

Authors :   N. Adir, E. Dobrovetsky, N. Lerner

Date :   17 Jan 02 (Deposition) - 06 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (6x)
Biol. Unit 3: A,B  (3x)
Biol. Unit 4: A,B  (2x)
Biol. Unit 5: A (2x),B (2x)

Keywords :   Cyanobacteria, Photosynthesis, Photosystem Ii, Light Harvesting Proteins, Thermostability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Adir, R. Vainer, N. Lerner
Refined Structure Of C-Phycocyanin From The Cyanobacterium Synechococcus Vulcanus At 1. 6 A: Insights Into The Role Of Solvent Molecules In Thermal Stability And Co-Factor Structure
Biochim. Biophys. Acta V. 1556 168 2002
PubMed-ID: 12460674 | Reference-DOI: 10.1016/S0005-2728(02)00359-6
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	2	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	2	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 2 (3, 24)

No.	Name	Count	Type	Full Name
1	BLA	6	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	12	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	6	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 3 (3, 12)

No.	Name	Count	Type	Full Name
1	BLA	3	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	6	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	3	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 4 (3, 8)

No.	Name	Count	Type	Full Name
1	BLA	2	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	4	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	2	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 5 (2, 6)

No.	Name	Count	Type	Full Name
1	BLA	-1	Ligand/Ion	BILIVERDINE IX ALPHA
2	CYC	4	Ligand/Ion	PHYCOCYANOBILIN
3	MEN	2	Mod. Amino Acid	N-METHYL ASPARAGINE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:59 , THR A:66 , SER A:72 , GLN A:73 , TYR A:74 , ALA A:75 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:90 , TYR A:110 , ILE A:118 , PHE A:122 , LEU A:124 , TRP A:128 , TYR A:129 , HOH A:489 , HOH A:490 , HOH A:506 , HOH A:528 , HOH A:624 , ARG B:57 , THR B:77 , ASN B:78	BINDING SITE FOR RESIDUE BLA A 484
2	AC2	SOFTWARE	LEU B:66 , MEN B:72 , ALA B:75 , ARG B:79 , ARG B:80 , ALA B:83 , CYS B:84 , ARG B:86 , ASP B:87 , ILE B:90 , TYR B:94 , ARG B:110 , LEU B:115 , LEU B:122 , THR B:124 , SER B:128 , HOH B:668 , HOH B:715 , HOH B:750 , HOH B:762 , HOH B:766	BINDING SITE FOR RESIDUE CYC B 584
3	AC3	SOFTWARE	ASN A:21 , LEU A:24 , ASP A:28 , ARG A:33 , GLN A:147 , HOH A:653 , LYS B:32 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , ARG B:43 , ALA B:144 , ASN B:145 , ASP B:146 , ILE B:150 , THR B:151 , GLY B:153 , CYS B:155 , HOH B:628 , HOH B:631 , HOH B:634 , HOH B:676	BINDING SITE FOR RESIDUE CYC B 555

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:162
 aligned with PHCA_THEEB | P50032 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           PHCA_THEEB     1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMVTYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 162
               SCOP domains d1ktpa_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1ktpA00 A:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains -----Phycobilisome-1ktpA01 A:6-174                                                                                                                                 Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ktp A   1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMITYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with PHCB_THEEB | P50033 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           PHCB_THEEB     1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 172
               SCOP domains d1ktpb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1ktpB00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains -----Phycobilisome-1ktpB01 B:6-172                                                                                                                                        -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktp B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   75

Legend:		→ Mismatch	(orange background)
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	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, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (PHCA_THEEB | P50032)

biological process
	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:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

Chain B (PHCB_THEEB | P50033)

biological process
	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:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

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