2B7R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF E378D MUTANT FLAVOCYTOCHROME C3

Authors :   K. L. Pankhurst, C. G. Mowat, E. L. Rothery, C. S. Miles, M. D. Walkinshaw, G. A. Reid, S. K. Chapman

Date :   05 Oct 05 (Deposition) - 23 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Flavocytochrome C3, Fumarate Reductase, Proton Delivery, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Pankhurst, C. G. Mowat, E. L. Rothery, J. M. Hudson, A. K. Jones, C. S. Miles, M. D. Walkinshaw, F. A. Armstrong, G. A. Reid, S. K. Chapman
A Proton Delivery Pathway In The Soluble Fumarate Reductase From Shewanella Frigidimarina.
J. Biol. Chem. V. 281 20589 2006
PubMed-ID: 16699170 | Reference-DOI: 10.1074/JBC.M603077200
(for further references see the PDB file header)

Molecule 1 - FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT
	Chains	:	A
	EC Number	:	1.3.99.1
	Engineered	:	YES
	Expression System	:	SHEWANELLA FRIGIDIMARINA
	Expression System Plasmid	:	PMMB503EH
	Expression System Strain	:	EG301
	Expression System Taxid	:	56812
	Expression System Vector Type	:	PLASMID
	Gene	:	FCC
	Mutation	:	YES
	Organism Scientific	:	SHEWANELLA FRIGIDIMARINA
	Organism Taxid	:	56812
	Synonym	:	FLAVOCYTOCHROME C3, FLAVOCYTOCHROME C, FCC3

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FUM	1	Ligand/Ion	FUMARIC ACID
3	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:506 , MET A:507 , GLY A:508 , GLU A:534 , THR A:536 , HOH A:1865	BINDING SITE FOR RESIDUE NA A 1810
2	AC2	SOFTWARE	CYS A:14 , CYS A:17 , HIS A:18 , SER A:73 , ALA A:74 , HIS A:75 , HOH A:2017 , HOH A:2022 , HOH A:2068 , HOH A:2272 , HOH A:2799 , HOH A:2800	BINDING SITE FOR RESIDUE HEM A 801
3	AC3	SOFTWARE	LEU A:4 , PHE A:7 , HIS A:8 , GLN A:12 , SER A:16 , CYS A:36 , CYS A:39 , HIS A:40 , HIS A:72 , TYR A:94 , HOH A:2277 , HOH A:2506 , HOH A:2645	BINDING SITE FOR RESIDUE HEM A 802
4	AC4	SOFTWARE	HIS A:40 , LEU A:43 , HIS A:52 , ALA A:57 , HIS A:58 , VAL A:66 , ALA A:67 , CYS A:68 , CYS A:71 , HIS A:72 , PHE A:90 , ASN A:91 , MET A:92 , HEM A:804 , HOH A:1890 , HOH A:2251 , HOH A:2827	BINDING SITE FOR RESIDUE HEM A 803
5	AC5	SOFTWARE	HIS A:54 , ASN A:56 , SER A:60 , HIS A:61 , CYS A:82 , SER A:84 , CYS A:85 , HIS A:86 , PHE A:88 , LEU A:167 , GLN A:338 , VAL A:374 , LYS A:431 , LYS A:434 , HEM A:803 , HOH A:1815 , HOH A:1830 , HOH A:1850 , HOH A:1885 , HOH A:1989 , HOH A:2004 , HOH A:2012 , HOH A:2302 , HOH A:2332	BINDING SITE FOR RESIDUE HEM A 804
6	AC6	SOFTWARE	VAL A:132 , GLY A:133 , GLY A:135 , GLY A:136 , ALA A:137 , GLU A:156 , LYS A:157 , GLU A:158 , GLY A:162 , GLY A:163 , ASN A:164 , ALA A:165 , LEU A:167 , ALA A:168 , ALA A:169 , GLY A:170 , GLY A:171 , ARG A:277 , GLY A:278 , ALA A:312 , THR A:313 , GLY A:314 , THR A:336 , GLN A:338 , ASP A:344 , MET A:375 , HIS A:504 , HIS A:505 , GLY A:533 , GLU A:534 , ARG A:544 , GLY A:547 , ASN A:548 , ALA A:549 , ILE A:550 , ILE A:553 , FUM A:1806 , HOH A:1814 , HOH A:1817 , HOH A:1818 , HOH A:1819 , HOH A:1844	BINDING SITE FOR RESIDUE FAD A 1805
7	AC7	SOFTWARE	GLY A:170 , HIS A:365 , THR A:377 , ASP A:378 , ARG A:402 , HIS A:504 , ARG A:544 , GLY A:546 , GLY A:547 , FAD A:1805	BINDING SITE FOR RESIDUE FUM A 1806

(no "SS Bond" information available for 2B7R)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:175	-	Trp A:176

(no "SAP(SNP)/Variant" information available for 2B7R)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	FRDA_SHEFR	9-91	1	A:9-91
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	FRDA_SHEFN	34-116	1	A:9-91

(no "Exon" information available for 2B7R)

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)
	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:568
 aligned with FRDA_SHEFN | Q07WU7 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:568
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585        
           FRDA_SHEFN    26 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 593
               SCOP domains d2b7ra1 A:1-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain                --------d2b7ra2 A:111-361,A:512-568 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                            d2b7ra3 A:362-504 Flavocytochrome c3 (respiratory fumarate reductase)                                                                          -------d2b7ra2 A:111-361,A:512-568                               SCOP domains
               CATH domains 2b7rA01 A:1-99 Flavocytochrome C3; Chain A                                                         ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined]                                                                                                                                                                                                  -----2b7rA03 A:365-502 Flavocytochrome C3; Chain A, domain 1                                                                                   ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined] CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhh..................hhhhh........hhhhhh....................hhhhhhhhhhhhhhhh...ee..eeee..hhhhhhhhhhhhhh...eeee........hhhhh...ee...hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh..eee..eeeeeeee.....eeeeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh...ee....eeeeeeee........hhhhhh..eee............hhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhh...ee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..................eeeeeeeeeeeee..eee.....eee.....eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------MULTIHEME_CYTC  PDB: A:9-91 UniProt: 34-116                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7r A   1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTDAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560

Chain A from PDB  Type:PROTEIN  Length:568
 aligned with FRDA_SHEFR | P0C278 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:568
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
           FRDA_SHEFR     1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLEEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWQRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
               SCOP domains d2b7ra1 A:1-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain                --------d2b7ra2 A:111-361,A:512-568 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                            d2b7ra3 A:362-504 Flavocytochrome c3 (respiratory fumarate reductase)                                                                          -------d2b7ra2 A:111-361,A:512-568                               SCOP domains
               CATH domains 2b7rA01 A:1-99 Flavocytochrome C3; Chain A                                                         ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined]                                                                                                                                                                                                  -----2b7rA03 A:365-502 Flavocytochrome C3; Chain A, domain 1                                                                                   ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined] CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhh..................hhhhh........hhhhhh....................hhhhhhhhhhhhhhhh...ee..eeee..hhhhhhhhhhhhhh...eeee........hhhhh...ee...hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh..eee..eeeeeeee.....eeeeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh...ee....eeeeeeee........hhhhhh..eee............hhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhh...ee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..................eeeeeeeeeeeee..eee.....eee.....eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------MULTIHEME_CYTC  PDB: A:9-91 UniProt: 9-91                                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7r A   1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTDAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560

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 '\|'

(no "Pfam Domain" information available for 2B7R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FRDA_SHEFN | Q07WU7)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0000104	succinate dehydrogenase activity	Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
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.
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).

Chain A (FRDA_SHEFR | P0C278)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0000104	succinate dehydrogenase activity	Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
biological process
	GO:0019645	anaerobic 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 other than oxygen to generate a transmembrane electrochemical gradient.
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:175 - Trp A:176	[ RasMol ]

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	2b7r
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	1.3.99.1
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1qjd	WILD-TYPE ENZYME
2b7s	THE SAME PROTEIN, R381K MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

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

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (9, 14)

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