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Title :   KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES

Authors :   A. Dolla, P. Arnoux, I. Protasevich, V. Lobachov, M. Brugna, M. T. Guidi Orticoni, R. Haser, M. Czjzek, A. Makarov, M. Brushi

Date :   08 Sep 98 (Deposition) - 04 May 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Mutant Cytochrome C3, Desulfovibrio Vulgaris Hildenborough, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dolla, P. Arnoux, I. Protasevich, V. Lobachov, M. Brugna, M. T. Giudici-Orticoni, R. Haser, M. Czjzek, A. Makarov, M. Bruschi
Key Role Of Phenylalanine 20 In Cytochrome C3: Structure, Stability, And Function Studies.
Biochemistry V. 38 33 1999
PubMed-ID: 9890880 | Reference-DOI: 10.1021/BI981593H
(for further references see the PDB file header)

Compounds

Molecule 1 - CYTOCHROME C3
	Cellular Location	:	PERIPLASMIC
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DESULFOVIBRIO DESULFURICANS
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	CYC
	Expression System Plasmid	:	PJRC800F20L
	Expression System Strain	:	G200
	Expression System Taxid	:	876
	Expression System Vector Type	:	BROAD-HOST RANGE
	Gene	:	CYC
	Mutation	:	YES
	Organism Scientific	:	DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH
	Organism Taxid	:	882
	Strain	:	HILDENBOROUGH
	Synonym	:	TETRA HEME CYTOCHROME, CYTOCHROME C3 (MR 13000)

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:11 , LEU A:20 , HIS A:22 , VAL A:28 , LYS A:29 , CYS A:30 , CYS A:33 , HIS A:34 , TYR A:43 , LYS A:45 , LEU B:9 , HEM B:110	BINDING SITE FOR RESIDUE HEM A 110
2	AC2	SOFTWARE	HIS A:35 , ASP A:42 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , HIS A:67 , MET A:69 , THR A:74 , LYS A:75 , PHE A:76	BINDING SITE FOR RESIDUE HEM A 111
3	AC3	SOFTWARE	HIS A:25 , SER A:78 , CYS A:79 , CYS A:82 , HIS A:83 , LYS A:104 , HOH A:249	BINDING SITE FOR RESIDUE HEM A 112
4	AC4	SOFTWARE	GLN A:16 , PRO A:17 , VAL A:18 , TYR A:65 , HIS A:70 , CYS A:79 , HIS A:83 , CYS A:100 , CYS A:105 , HIS A:106 , HOH A:245 , PRO B:17 , CYS B:100 , HEM B:113	BINDING SITE FOR RESIDUE HEM A 113
5	AC5	SOFTWARE	HIS A:22 , HEM A:110 , LEU B:9 , MET B:11 , HIS B:22 , HIS B:25 , CYS B:30 , CYS B:33 , HIS B:34 , TYR B:43 , ARG B:44 , LYS B:45 , HOH B:339	BINDING SITE FOR RESIDUE HEM B 110
6	AC6	SOFTWARE	HIS B:35 , VAL B:37 , LYS B:45 , CYS B:46 , CYS B:51 , HIS B:52 , HIS B:67 , THR B:74 , LYS B:75 , PHE B:76 , LYS B:77	BINDING SITE FOR RESIDUE HEM B 111
7	AC7	SOFTWARE	HIS B:25 , LYS B:77 , CYS B:79 , CYS B:82 , HIS B:83 , VAL B:86 , LYS B:104	BINDING SITE FOR RESIDUE HEM B 112
8	AC8	SOFTWARE	GLN A:16 , PRO A:17 , HEM A:113 , MET B:11 , GLN B:16 , VAL B:18 , TYR B:65 , HIS B:70 , CYS B:79 , LEU B:97 , CYS B:100 , CYS B:105 , HIS B:106	BINDING SITE FOR RESIDUE HEM B 113

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	CYC3_DESVH	47-110	2	A:25-88 B:25-88

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	CYC3_DESVH	47-110	1	A:25-88 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	CYC3_DESVH	47-110	1	- B:25-88

Biological Unit 3 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	CYC3_DESVH	47-110	8	A:25-88 B:25-88

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:101
 aligned with CYC3_DESVH | P00131 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:101
                                    38        48        58        68        78        88        98       108       118       128 
           CYC3_DESVH    29 DGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 129
               SCOP domains d1mdva_ A: Cytochrome c3                                                                              SCOP domains
               CATH domains 1mdvA00 A:7-107 Cytochrome C3                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........ee........hhhh..ee..ee.......................hhhhhh........hhhhhhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------MULTIHEME_CYTC  PDB: A:25-88 UniProt: 47-110                    ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1mdv A   7 DGLKMEATKQPVVLNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 107
                                    16        26        36        46        56        66        76        86        96       106

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with CYC3_DESVH | P00131 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:100
                                    39        49        59        69        79        89        99       109       119       129
           CYC3_DESVH    30 GLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 129
               SCOP domains d1mdvb_ B: Cytochrome c3                                                                             SCOP domains
               CATH domains 1mdvB00 B:8-107 Cytochrome C3                                                                        CATH domains
           Pfam domains (1) Cytochrom_CIII-1mdvB01 B:8-106                                                                     - Pfam domains (1)
           Pfam domains (2) Cytochrom_CIII-1mdvB02 B:8-106                                                                     - Pfam domains (2)
         Sec.struct. author ..ee......ee..........hhhh...............................hhhhhh........hhhhhhhhh...hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------MULTIHEME_CYTC  PDB: B:25-88 UniProt: 47-110                    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1mdv B   8 GLKMEATKQPVVLNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 107
                                    17        27        37        47        57        67        77        87        97       107

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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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYC3_DESVH | P00131)

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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