1J0P - JenaLib

Title :   THREE DIMENSIONAL STRUCTURE OF THE Y43L MUTANT OF TETRAHEME CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS MIYAZAKI F

Authors :   K. Ozawa, F. Yasukawa, J. Kumagai, T. Ohmura, M. A. Cusanvich, Y. Tomimoto, H. Ogata, Y. Higuchi, H. Akutsu

Date :   19 Nov 02 (Deposition) - 19 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.91

Chains :   Asym./Biol. Unit : A

Keywords :   Tetraheme Cytochrome C3, High Resolution X-Ray Structure, Y43L Mutant, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ozawa, Y. Takayama, F. Yasukawa, T. Ohmura, M. A. Cusanovich, Y. Tomimoto, H. Ogata, Y. Higuchi, H. Akutsu
Role Of The Aromatic Ring Of Tyr43 In Tetraheme Cytochrome C(3) From Desulfovibrio Vulgaris Miyazaki F
Biophys. J. V. 85 3367 2003
PubMed-ID: 14581238
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 23)

Sites (23, 23)

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:0 , LYS A:40 , LYS A:101 , HOH A:3032 , HOH A:3063 , HOH A:3066 , HOH A:3141 , HOH A:3265	BINDING SITE FOR RESIDUE SO4 A 2501
02	AC2	SOFTWARE	ALA A:0 , LYS A:40 , LYS A:57 , EOH A:2012 , HOH A:3003 , HOH A:3067 , HOH A:3109 , HOH A:3174 , HOH A:3176 , HOH A:3276	BINDING SITE FOR RESIDUE SO4 A 2502
03	AC3	SOFTWARE	MET A:11 , ASP A:12 , LYS A:13 , THR A:14 , GLN A:16 , PRO A:17 , VAL A:18 , ASN A:38 , GLY A:39 , TYR A:65 , TYR A:66 , HIS A:70 , CYS A:79 , VAL A:80 , HIS A:83 , LEU A:97 , THR A:98 , GLY A:99 , CYS A:100 , CYS A:105 , HIS A:106 , EOH A:2003 , HOH A:3014 , HOH A:3081 , HOH A:3082 , HOH A:3125 , HOH A:3212	BINDING SITE FOR RESIDUE HEM A 1004
04	AC4	SOFTWARE	CYS A:33 , HIS A:35 , ASP A:42 , GLN A:44 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , HIS A:67 , ALA A:68 , THR A:74 , LYS A:75 , PHE A:76 , EOH A:2006 , HOH A:3092 , HOH A:3137 , HOH A:3168 , HOH A:3200 , HOH A:3321 , HOH A:3333 , HOH A:3337	BINDING SITE FOR RESIDUE HEM A 1002
05	AC5	SOFTWARE	PRO A:2 , LYS A:3 , ALA A:4 , PRO A:5 , LEU A:9 , MET A:11 , PHE A:20 , HIS A:22 , HIS A:25 , VAL A:28 , CYS A:30 , CYS A:33 , HIS A:34 , LEU A:43 , LYS A:45 , CYS A:46 , HEM A:1003 , EOH A:2017 , HOH A:3013 , HOH A:3037 , HOH A:3187 , HOH A:3195 , HOH A:3197 , HOH A:3326	BINDING SITE FOR RESIDUE HEM A 1001
06	AC6	SOFTWARE	VAL A:18 , ASN A:21 , THR A:24 , HIS A:25 , CYS A:79 , CYS A:82 , HIS A:83 , LYS A:93 , LYS A:104 , HEM A:1001 , EOH A:2008 , HOH A:3020 , HOH A:3023 , HOH A:3101 , HOH A:3241 , HOH A:3251 , HOH A:3332	BINDING SITE FOR RESIDUE HEM A 1003
07	AC7	SOFTWARE	CYS A:51 , HOH A:3007 , HOH A:3046 , HOH A:3316	BINDING SITE FOR RESIDUE EOH A 2001
08	AC8	SOFTWARE	HIS A:70 , LYS A:72 , HOH A:3165 , HOH A:3292	BINDING SITE FOR RESIDUE EOH A 2002
09	AC9	SOFTWARE	GLN A:16 , CYS A:100 , HEM A:1004 , HOH A:3128	BINDING SITE FOR RESIDUE EOH A 2003
10	BC1	SOFTWARE	LYS A:15 , EOH A:2005 , HOH A:3107 , HOH A:3113 , HOH A:3140 , HOH A:3179 , HOH A:3263	BINDING SITE FOR RESIDUE EOH A 2004
11	BC2	SOFTWARE	ALA A:4 , PRO A:5 , EOH A:2004 , HOH A:3073	BINDING SITE FOR RESIDUE EOH A 2005
12	BC3	SOFTWARE	GLY A:50 , HEM A:1002 , HOH A:3139	BINDING SITE FOR RESIDUE EOH A 2006
13	BC4	SOFTWARE	LYS A:72 , GLY A:73 , GLU A:85 , THR A:86	BINDING SITE FOR RESIDUE EOH A 2007
14	BC5	SOFTWARE	VAL A:19 , ASN A:21 , LYS A:104 , HEM A:1003 , HOH A:3019 , HOH A:3225 , HOH A:3281	BINDING SITE FOR RESIDUE EOH A 2008
15	BC6	SOFTWARE	ALA A:27 , EOH A:2015 , HOH A:3099 , HOH A:3310	BINDING SITE FOR RESIDUE EOH A 2009
16	BC7	SOFTWARE	TYR A:66 , HOH A:3043 , HOH A:3156 , HOH A:3204	BINDING SITE FOR RESIDUE EOH A 2010
17	BC8	SOFTWARE	HOH A:3153 , HOH A:3304	BINDING SITE FOR RESIDUE EOH A 2011
18	BC9	SOFTWARE	LYS A:40 , LYS A:58 , SO4 A:2502	BINDING SITE FOR RESIDUE EOH A 2012
19	CC1	SOFTWARE	ASP A:7 , ASN A:21 , SER A:61	BINDING SITE FOR RESIDUE EOH A 2013
20	CC2	SOFTWARE	LYS A:29 , LYS A:63 , HOH A:3186 , HOH A:3255 , HOH A:3277 , HOH A:3352	BINDING SITE FOR RESIDUE EOH A 2014
21	CC3	SOFTWARE	THR A:24 , HIS A:25 , LYS A:26 , ALA A:27 , VAL A:28 , EOH A:2009 , HOH A:3189	BINDING SITE FOR RESIDUE EOH A 2015
22	CC4	SOFTWARE	ASP A:32 , HOH A:3132 , HOH A:3192	BINDING SITE FOR RESIDUE EOH A 2016
23	CC5	SOFTWARE	LEU A:9 , LYS A:10 , LYS A:45 , HEM A:1001 , HOH A:3012 , HOH A:3213 , HOH A:3287	BINDING SITE FOR RESIDUE EOH A 2017

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/Biological Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:108
 aligned with CYC3_DESVM | P00132 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:108
                                    32        42        52        62        72        82        92       102       112       122        
           CYC3_DESVM    23 AAPKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS 130
               SCOP domains d1j0pa_ A: Cytochrome c3                                                                                     SCOP domains
               CATH domains 1j0pA00 A:0-107 Cytochrome C3                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee......eeehhhhh...hhhhh..ee..ee......................hhhhhhhh......hhhhhhhhhhh.hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1j0p A   0 AAPKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDLQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS 107
                                     9        19        29        39        49        59        69        79        89        99

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	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 (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYC3_DESVM | P00132)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009061	anaerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
	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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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