2BQ4 - JenaLib

Title :   CRYSTAL STRUCTURE OF TYPE I CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS

Authors :   M. Czjzek, L. Pieulle, X. Morelli, F. Guerlesquin, E. C. Hatchikian

Date :   27 Apr 05 (Deposition) - 19 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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

Keywords :   Basic Cytochrome C3, Electron Transfer, Sulfate Reducing Bacteria, Sad, Heme, Iron, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Pieulle, X. Morelli, P. Gallice, E. Lojou, P. Barbier, M. Czjzek, P. Bianco, F. Guerlesquin, E. C. Hatchikian
The Type I / Type Ii Cytochrome C(3) Complex: An Electron Transfer Link In The Hydrogen-Sulfate Reduction Pathway.
J. Mol. Biol. V. 354 73 2005
PubMed-ID: 16226767 | Reference-DOI: 10.1016/J.JMB.2005.09.036

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:10 , LEU A:12 , GLU A:20 , TYR A:21 , HEC A:1118	BINDING SITE FOR RESIDUE CA A1119
02	AC2	SOFTWARE	ASP B:10 , LEU B:12 , GLU B:20 , TYR B:21 , HEC B:1119	BINDING SITE FOR RESIDUE CA B1120
03	AC3	SOFTWARE	PRO A:1 , GLN A:2 , VAL A:3 , PRO A:4 , HIS A:11 , PHE A:25 , HIS A:27 , HIS A:30 , ALA A:39 , CYS A:40 , CYS A:43 , HIS A:44 , GLY A:54 , HEC A:1117 , HOH A:2130	BINDING SITE FOR RESIDUE HEC A1115
04	AC4	SOFTWARE	CYS A:43 , HIS A:44 , HIS A:45 , LYS A:46 , CYS A:56 , GLU A:59 , GLY A:60 , CYS A:61 , HIS A:62 , ALA A:81 , SER A:84 , SER A:86 , MET A:88 , SER A:89 , HOH A:2131 , HOH A:2132 , HOH A:2133 , LYS B:28	BINDING SITE FOR RESIDUE HEC A1116
05	AC5	SOFTWARE	PHE A:25 , ALA A:29 , HIS A:30 , SER A:32 , LEU A:33 , THR A:35 , CYS A:43 , PRO A:87 , MET A:88 , SER A:89 , CYS A:90 , CYS A:93 , HIS A:94 , MET A:97 , THR A:103 , THR A:104 , GLY A:105 , PRO A:106 , HEC A:1115 , HOH A:2134	BINDING SITE FOR RESIDUE HEC A1117
06	AC6	SOFTWARE	ILE A:9 , ASP A:10 , HIS A:11 , LEU A:12 , SER A:13 , ASN A:14 , LEU A:19 , GLU A:20 , TYR A:21 , VAL A:23 , PHE A:68 , ALA A:70 , MET A:79 , PHE A:82 , HIS A:83 , CYS A:90 , GLN A:91 , HIS A:94 , PRO A:106 , THR A:107 , CYS A:109 , CYS A:112 , HIS A:113 , CA A:1119	BINDING SITE FOR RESIDUE HEC A1118
07	AC7	SOFTWARE	GLN B:2 , HIS B:11 , PHE B:25 , HIS B:27 , HIS B:30 , ALA B:39 , CYS B:40 , CYS B:43 , HIS B:44 , ILE B:53 , GLY B:54 , GLY B:55 , HEC B:1118 , HOH B:2010 , HOH B:2081 , HOH B:2141 , HOH B:2142 , HOH B:2143 , HOH B:2144 , HOH B:2145	BINDING SITE FOR RESIDUE HEC B1116
08	AC8	SOFTWARE	LYS A:28 , CYS B:43 , HIS B:45 , LYS B:46 , GLY B:55 , CYS B:56 , GLU B:59 , GLY B:60 , CYS B:61 , HIS B:62 , PRO B:75 , ALA B:81 , SER B:84 , SER B:86 , MET B:88 , SER B:89 , HOH B:2146 , HOH B:2147	BINDING SITE FOR RESIDUE HEC B1117
09	AC9	SOFTWARE	PHE B:25 , ALA B:29 , HIS B:30 , SER B:32 , LEU B:33 , THR B:35 , CYS B:43 , PRO B:87 , SER B:89 , CYS B:90 , CYS B:93 , HIS B:94 , MET B:97 , THR B:103 , THR B:104 , GLY B:105 , PRO B:106 , GLN B:115 , HEC B:1116 , HOH B:2148 , HOH B:2149	BINDING SITE FOR RESIDUE HEC B1118
10	BC1	SOFTWARE	ILE B:9 , ASP B:10 , HIS B:11 , LEU B:12 , SER B:13 , ASN B:14 , LEU B:19 , GLU B:20 , TYR B:21 , VAL B:23 , PHE B:68 , ALA B:70 , MET B:79 , PHE B:82 , HIS B:83 , CYS B:90 , GLN B:91 , HIS B:94 , PRO B:106 , THR B:107 , CYS B:109 , CYS B:112 , HIS B:113 , CA B:1120	BINDING SITE FOR RESIDUE HEC B1119

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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:114
 aligned with CYC3B_DESAF | P94691 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:114
                                    34        44        54        64        74        84        94       104       114       124       134    
          CYC3B_DESAF    25 PQVPADVVIDHLSNPNAKLEYKVKFSHKAHASLGTDAAACQKCHHKWDGKSEIGGCATEGCHADTTSFKATEKDPKFLMTAFHSKSPMSCQGCHKEMKTAKKTTGPTACAQCHN 138
               SCOP domains d2bq4a_ A: automated matches                                                                                       SCOP domains
               CATH domains 2bq4A00 A:1-114 Cytochrome C3                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......hhhhh..eee.hhhhhhhh.hhhhhhh..................................hhhhhhhh....hhhhhhhhhhhhh......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------MULTIHEME_CYTC  PDB: A:35-99 UniProt: 59-123                     --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2bq4 A   1 PQVPADVVIDHLSNPNAKLEYKVKFSHKAHASLGTDAAACQKCHHKWDGKSEIGGCATEGCHADTTSFKATEKDPKFLMTAFHSKSPMSCQGCHKEMKTAKKTTGPTACAQCHN 114
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with CYC3B_DESAF | P94691 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:115
                                    34        44        54        64        74        84        94       104       114       124       134     
          CYC3B_DESAF    25 PQVPADVVIDHLSNPNAKLEYKVKFSHKAHASLGTDAAACQKCHHKWDGKSEIGGCATEGCHADTTSFKATEKDPKFLMTAFHSKSPMSCQGCHKEMKTAKKTTGPTACAQCHNQ 139
               SCOP domains d2bq4b_ B: automated matches                                                                                        SCOP domains
               CATH domains 2bq4B00 B:1-115 Cytochrome C3                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......hhhhh..eee.hhhhhhhh.hhhhhhh..................................hhhhhhhh....hhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------MULTIHEME_CYTC  PDB: B:35-99 UniProt: 59-123                     ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2bq4 B   1 PQVPADVVIDHLSNPNAKLEYKVKFSHKAHASLGTDAAACQKCHHKWDGKSEIGGCATEGCHADTTSFKATEKDPKFLMTAFHSKSPMSCQGCHKEMKTAKKTTGPTACAQCHNQ 115
                                    10        20        30        40        50        60        70        80        90       100       110

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYC3B_DESAF | P94691)

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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	2bq4
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1a2i	SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS ( HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES
1e39	FLAVOCYTOCHROME C3 FROM SHEWANELLA FRIGIDIMARINA HISTIDINE 3
1gm4	OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
1gmb	REDUCED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
1gx7	BEST MODEL OF THE ELECTRON TRANSFER COMPLEX BETWEEN CYTOCHROME C3 AND [FE]-HYDROGENASE
1gyo	CRYSTAL STRUCTURE OF THE DI-TETRAHEME CYTOCHROME C3 FROM DESULFOVIBRIO GIGAS AT 1 .2 E RESOLUTION
1i77	CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ESSEX 6
1it1	SOLUTION STRUCTURES OF FERROCYTOCHROME C3 FROMDESULFOVIBRIO VULGARIS MIYAZAKI F
1j0o	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD TYPETETRAHEME CYTOCHROME C3 FROM DESULFOVIBRIO VULGARISMIYAZAKI F
1j0p	THREE DIMENSIONAL STRUCTURE OF THE Y43L MUTANT OF TETRAHEMECYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS MIYAZAKI F
1jrx	CRYSTAL STRUCTURE OF ARG402ALA MUTANT FLAVOCYTOCHROME C3FROM SHEWANELLA FRIGIDIMARINA
1jry	CRYSTAL STRUCTURE OF ARG402LYS MUTANT FLAVOCYTOCHROME C3FROM SHEWANELLA FRIGIDIMARINA
1jrz	CRYSTAL STRUCTURE OF ARG402TYR MUTANT FLAVOCYTOCHROME C3FROM SHEWANELLA FRIGIDIMARINA
1kss	CRYSTAL STRUCTURE OF HIS505ALA MUTANT FLAVOCYTOCHROME C3FROM SHEWANELLA FRIGIDIMARINA
1ksu	CRYSTAL STRUCTURE OF HIS505TYR MUTANT FLAVOCYTOCHROME C3FROM SHEWANELLA FRIGIDIMARINA
1lj1	CRYSTAL STRUCTURE OF Q363F/R402A MUTANT FLAVOCYTOCHROME C3
1m1p	P21 CRYSTAL STRUCTURE OF THE TETRAHEME CYTOCHROME C3 FROMSHEWANELLA ONEIDENSIS MR1
1m64	CRYSTAL STRUCTURE OF Q363F MUTANT FLAVOCYTOCHROME C3
1mdv	KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES
1p2e	H61A MUTANT OF FLAVOCYTOCHROME C3
1p2h	H61M MUTANT OF FLAVOCYTOCHROME C3
1q9i	THE A251C:S430C DOUBLE MUTANT OF FLAVOCYTOCHROME C3 FROMSHEWANELLA FRIGIDIMARINA
1qjd	FLAVOCYTOCHROME C3 FROM SHEWANELLA FRIGIDIMARINA
1qn0	SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERROCYTOCHROME C3, NMR, 20 STRUCTURES
1qn1	SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERRICYTOCHROME C3, NMR, 15 STRUCTURES
1qo8	THE STRUCTURE OF THE OPEN CONFORMATION OF A FLAVOCYTOCHROME C3 FUMARATE REDUCTASE
1up9	REDUCED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
1upd	OXIDIZED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
1w7o	CYTOCHROME C3 FROM DESULFOMICROBIUM BACULATUS
1wad	CYTOCHROME C3 WITH 4 HEME GROUPS AND ONE CALCIUM ION
1wr5	THREE DIMENSIONAL STRUCTURE OF THE E41K MUTANT OF TETRAHEMECYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS MIYAZAKI F
2bpn	SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS ( HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES
2cth	CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
3cao	OXIDISED STRUCTURE OF ACIDIC CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS
3car	REDUCED STRUCTURE OF ACIDIC CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS
3cyr	CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P

Description