1MZ4 - JenaLib

Title :   CRYSTAL STRUCTURE OF CYTOCHROME C550 FROM THERMOSYNECHOCOCCUS ELONGATUS

Authors :   C. A. Kerfeld, M. R. Sawaya, H. Bottin, K. T. Tran, M. Sugiura, D. Kirilov D. Krogmann, T. O. Yeates, A. Boussac

Date :   05 Oct 02 (Deposition) - 23 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Psii Associated Cytochrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Kerfeld, M. R. Sawaya, H. Bottin, K. T. Tran, M. Sugiura, D. Cascio A. Desbois, T. O. Yeates, D. Kirilovsky, A. Boussac
Structural And Epr Characterization Of The Soluble Form Of Cytochrome C-550 And Of The Psbv2 Gene Product From The Cyanobacterium Thermosynechococcus Elongatus.
Plant Cell. Physiol. V. 44 697 2003
PubMed-ID: 12881497 | Reference-DOI: 10.1093/PCP/PCG084

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:4 , PRO A:5 , GLU A:6 , GLU A:23 , GLU A:87 , ILE A:88 , ALA A:89 , GLU A:90 , HOH A:167 , HOH A:185	BINDING SITE FOR RESIDUE PO4 A 145
02	AC2	SOFTWARE	THR A:22 , GLU A:23 , LYS A:24 , GLU A:90 , HOH A:169 , HOH A:172 , HOH A:181	BINDING SITE FOR RESIDUE PO4 A 146
03	AC3	SOFTWARE	TYR A:26 , LYS A:30 , ASP A:83 , GLU A:85 , GLN A:86 , GLU A:122 , LEU A:126 , PO4 A:148 , HOH A:245	BINDING SITE FOR RESIDUE PO4 A 147
04	AC4	SOFTWARE	HIS A:118 , GLU A:122 , LEU A:126 , PO4 A:147 , HOH A:176 , HOH A:256	BINDING SITE FOR RESIDUE PO4 A 148
05	AC5	SOFTWARE	LYS A:24 , GLU A:28 , HOH A:159 , HOH A:181	BINDING SITE FOR RESIDUE PO4 A 149
06	AC6	SOFTWARE	LYS A:30 , LEU A:52 , THR A:81 , TYR A:82 , HEM A:151 , HOH A:162 , HOH A:208 , HOH A:248	BINDING SITE FOR RESIDUE BCT A 150
07	AC7	SOFTWARE	ALA A:36 , CYS A:37 , SER A:39 , CYS A:40 , HIS A:41 , THR A:46 , THR A:48 , LEU A:52 , ASP A:53 , LEU A:54 , THR A:58 , LEU A:59 , LEU A:72 , TYR A:75 , TYR A:82 , HIS A:92 , ILE A:115 , ILE A:119 , GOL A:141 , BCT A:150 , HOH A:153 , HOH A:154	BINDING SITE FOR RESIDUE HEM A 151
08	AC8	SOFTWARE	THR A:56 , ARG A:105 , HOH A:220 , HOH A:229 , HOH A:236 , HOH A:239	BINDING SITE FOR RESIDUE GOL A 140
09	AC9	SOFTWARE	LYS A:24 , GLU A:28 , ARG A:31 , THR A:48 , ASN A:49 , HEM A:151	BINDING SITE FOR RESIDUE GOL A 141
10	BC1	SOFTWARE	ASN A:13 , SER A:14 , GLY A:16 , ASP A:67 , ASN A:68 , ARG A:105 , HOH A:216	BINDING SITE FOR RESIDUE GOL A 142
11	BC2	SOFTWARE	ARG A:31 , TYR A:35	BINDING SITE FOR RESIDUE GOL A 143
12	BC3	SOFTWARE	GLU A:87 , ARG A:96	BINDING SITE FOR RESIDUE GOL A 144

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with CY550_THEEB | P0A386 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:131
                                    36        46        56        66        76        86        96       106       116       126       136       146       156 
          CY550_THEEB    27 AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWG 157
               SCOP domains d1mz4a_ A: Cytochrome c550                                                                                                          SCOP domains
               CATH domains 1mz4A00 A:1-131 Cytochrome c                                                                                                        CATH domains
               Pfam domains -------------------------Cytochrom_C-1mz4A01 A:26-121                                                                    ---------- Pfam domains
         Sec.struct. author ...hhhhheee......eee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhh......hhhhhhhhhhh...............hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------CYTC  PDB: A:24-123 UniProt: 50-149                                                                 -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mz4 A   1 AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWG 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CY550_THEEB | P0A386)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0018063	cytochrome c-heme linkage	The linkage of cytochromes and other heme proteins to heme.
	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:0019684	photosynthesis, light reaction	The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0009523	photosystem II	A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center.
	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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