4YRY - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   INSIGHTS INTO FLAVIN-BASED ELECTRON BIFURCATION VIA THE NADH-DEPENDENT REDUCED FERREDOXIN-NADP OXIDOREDUCTASE STRUCTURE

Authors :   U. Ermler, R. K. Thauer, J. K. Demmer, H. Huang, S. Wang, U. Demmer

Date :   16 Mar 15 (Deposition) - 08 Jul 15 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Demmer, H. Huang, S. Wang, U. Demmer, R. K. Thauer, U. Ermler
Insights Into Flavin-Based Electron Bifurcation Via The Nadh-Dependent Reduced Ferredoxin:Nadp Oxidoreductase Structure.
J. Biol. Chem. V. 290 21985 2015
PubMed-ID: 26139605 | Reference-DOI: 10.1074/JBC.M115.656520

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE B (NAD(+)), ELECTRON TRANSFER SUBUNIT HOMOLOG
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-51B(+)
	Expression System Taxid	:	469008
	Expression System Variant	:	C41
	Gene	:	TM_1639
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	DIHYDROOROTATE OXIDASE B,ELECTRON TRANSFER SUBUNIT HOMOLOG

Molecule 2 - DIHYDROPYRIMIDINE DEHYDROGENASE SUBUNIT A
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	C41
	Gene	:	THEMA_06045
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	SF4	4	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	PO4	-1	Ligand/Ion	PHOSPHATE ION
5	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (5, 7)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:218 , VAL A:219 , ASP A:220 , GLY A:221 , GLY A:223 , MET A:224 , CYS A:225 , GLY A:226 , ALA A:227 , CYS A:228 , CYS A:240	binding site for residue FES A 501
02	AC2	SOFTWARE	PHE A:38 , GLU A:48 , PRO A:51 , LEU A:52 , THR A:53 , VAL A:67 , VAL A:68 , LYS A:69 , VAL A:71 , GLY A:72 , LYS A:73 , THR A:74 , THR A:75 , ASN A:215 , PRO A:216 , MET A:218 , LEU A:260 , GLN A:266 , ILE A:269 , NAD A:503 , HOH A:604	binding site for residue FAD A 502
03	AC3	SOFTWARE	LYS A:69 , GLY A:111 , GLY A:112 , VAL A:113 , GLY A:114 , THR A:117 , GLY A:137 , ALA A:138 , ARG A:139 , VAL A:170 , VAL A:171 , VAL A:190 , GLY A:191 , PRO A:192 , ILE A:194 , MET A:195 , MET A:196 , PHE A:198 , SER A:213 , ASN A:215 , FAD A:502 , HOH A:601	binding site for residue NAD A 503
04	AC4	SOFTWARE	CYS B:39 , LEU B:40 , CYS B:42 , CYS B:47 , CYS B:100 , VAL B:101 , VAL B:102	binding site for residue SF4 B 501
05	AC5	SOFTWARE	CYS B:51 , CYS B:90 , GLN B:95 , CYS B:96 , GLU B:117	binding site for residue SF4 B 502
06	AC6	SOFTWARE	VAL B:89 , PRO B:91 , GLY B:147 , SER B:148 , GLY B:149 , PRO B:150 , ALA B:151 , GLU B:170 , ALA B:171 , PHE B:172 , GLY B:177 , VAL B:178 , TYR B:181 , ILE B:183 , ARG B:187 , THR B:211 , VAL B:213 , GLY B:232 , THR B:233 , GLY B:234 , ASN B:289 , THR B:290 , GLN B:393 , LEU B:399 , GLY B:432 , ASP B:433 , ALA B:439 , THR B:440 , VAL B:441 , ALA B:444 , HOH B:608 , HOH B:609 , HOH B:621	binding site for residue FAD B 503
07	AC7	SOFTWARE	VAL C:219 , ASP C:220 , GLY C:221 , GLY C:223 , MET C:224 , CYS C:225 , GLY C:226 , CYS C:228 , CYS C:240	binding site for residue FES C 501
08	AC8	SOFTWARE	GLU C:48 , ILE C:50 , PRO C:51 , LEU C:52 , THR C:53 , VAL C:67 , VAL C:68 , LYS C:69 , VAL C:71 , GLY C:72 , LYS C:73 , THR C:74 , THR C:75 , ILE C:115 , ASN C:215 , PRO C:216 , ILE C:217 , MET C:218 , LEU C:260 , GLN C:266 , GLU C:267 , SER C:270 , HOH C:611	binding site for residue FAD C 502
09	AC9	SOFTWARE	CYS D:39 , LEU D:40 , CYS D:42 , CYS D:47 , CYS D:100 , VAL D:101	binding site for residue SF4 D 501
10	AD1	SOFTWARE	CYS D:51 , CYS D:90 , GLN D:95 , CYS D:96 , GLU D:117	binding site for residue SF4 D 502
11	AD2	SOFTWARE	VAL D:89 , GLY D:147 , SER D:148 , GLY D:149 , PRO D:150 , ALA D:151 , PHE D:169 , GLU D:170 , ALA D:171 , VAL D:178 , GLY D:182 , ILE D:183 , ARG D:187 , THR D:211 , VAL D:212 , VAL D:213 , GLY D:232 , THR D:233 , GLY D:234 , LEU D:258 , ASN D:289 , THR D:290 , ASP D:293 , GLY D:432 , ASP D:433 , ALA D:439 , THR D:440 , VAL D:441 , NAD D:504 , HOH D:612 , HOH D:618	binding site for residue FAD D 503
12	AD3	SOFTWARE	LYS D:239 , GLY D:288 , ASN D:289 , THR D:290 , TYR D:310 , ARG D:311 , ARG D:371 , PRO D:372 , ILE D:391 , GLY D:392 , ALA D:438 , ALA D:439 , FAD D:503	binding site for residue NAD D 504
13	AD4	SOFTWARE	ARG D:62 , LYS D:63 , ASP D:66 , LYS D:68	binding site for residue PO4 D 505

(no "SS Bond" information available for 4YRY)

Asymmetric Unit

No.	Residues
1	Gly A:92	-	Pro A:93
2	Gly A:243	-	Pro A:244
3	Lys B:133	-	Pro B:134
4	Pro B:175	-	Gly B:176
5	Thr B:237	-	Pro B:238
6	Phe B:269	-	Pro B:270
7	Gly C:92	-	Pro C:93
8	Gly C:243	-	Pro C:244
9	Thr D:237	-	Pro D:238
10	Phe D:269	-	Pro D:270

(no "SAP(SNP)/Variant" information available for 4YRY)

(no "PROSITE Motif" information available for 4YRY)

(no "Exon" information available for 4YRY)

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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee....eeeeeeehhhhhhh.....eeeee.......eeee..eee....eeeeeee..hhhhhhhhhh.......eeeeee..........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhheeee...........hhhhhhh.........eeee.hhhhhhhhhhhhhh....eeee...............eeee..eeee......eee....hhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yry A   1 MGGTALNEIVKKVKIAEDVFDFWIHSPSVSKEARPGQFVVIRLHEKGERIPLTVADTKPEEGLFRMVVKVVGKTTHELSLKKEGDTILDVVGPLGNPSEIENYGNVLLVGGGVGIATLYPIAKALKEAGNNITTVLGARTKDYLIMVDEFKEISDVLLVTDDGSAGMKGVVTDAMDKLFRERKFDICWAVGPTIMMKFCTLKAREFGVPIWVSLNPIMVDGTGMCGACRVTVSGQIKFACVDGPEFRGEEVDWDELLKRLAQYREQEKISYERFLK 276
                                    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

Chain B from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhh..........hhhhhhhhhh.......hhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhh.......hhhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhhhhh..eeeee......hhhhh........hhhhhhhhhhhhhhh..eee.........hhhhhhhhh.eeee...................eeehhhhhhhhh..hhhhh...........eeeee..hhhhhhhhhhhhh....eeeee..........hhhhhhhhhhh..eee..eeeeeeee.....eeeeeeeeeee..........eeeeeeeeeeee..eeee......hhhhhhh.........................eee.hhhhhh..hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yry B   1 MKNRKTPMKEQSPESRRRNFEEVALGYTLEEALEEAQRCLQCPTHPCVSGCPVEIDIPGFIRKLRDGKLEESYRILKSYNNLPAVCGRVCPQEVQCESRCVVGKMKDSEPVAIGRLERFVADWAAENLEEDVKPLAGSKKEKVAVVGSGPAGLTAAADLAKMGYHVDIFEAFHKPGGVLVYGIPEFRLPKRIVEREVSYIRKLGVNFHLNTVVGKTVKVKELLSEYDAVFIGTGAGTPKFMGIPGTNLNGVYSANEFLTRVNLMKAYLFPEYDTPIRVGKKVAVIGAGNTAMDAARSALRLGAEKVYIVYRRTEREMPARREEYHHALEEGIEFLWLTLPIRYIGDANGNVEAMECVRMELKEADGSGRPRPVPIEGSNFVLEVDMVIEAIGQGPNRVLLSEFPGLELNERGYIKADEDTGATSVKGVFAGGDIVTGAATVIKAMGAGKKAAQFIHSYLTGEWNPWQK 468
                                    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

Chain C from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.......eeeeeeehhhhhhhh....eeeee.......eeee..eee....eeeeeee..hhhhhhhhh........eeeeee..........eeeeee......hhhhhhhhhhhh..eeeeee..........hhhhhhhhheeee....................eeeee.hhhhhh.......eeee...............eeee..eeee......eee.hhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yry C   1 MGGTALNEIVKKVKIAEDVFDFWIHSPSVSKEARPGQFVVIRLHEKGERIPLTVADTKPEEGLFRMVVKVVGKTTHELSLKKEGDTILDVVGPLGNPSEIENYGNVLLVGGGVGIATLYPIAKALKEAGNNITTVLGARTKDYLIMVDEFKEISDVLLVTDDGSAGMKGVVTDRERKFDICWAVGPTIMMKFCTFGVPIWVSLNPIMVDGTGMCGACRVTVSGQIKFACVDGPEFRGEEVDWDELLKRLAQYREQEKISYERFLK 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  ||   186       196   ||  211       221       231       241       251       261       271     
                                                                                                                                                                                                      173|                 200|                                                                      
                                                                                                                                                                                                       180                  206

Chain D from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhh..........hhhhhhhhhhh......hhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhh.........hhhhh.......hhhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhhhhh..eeeee.......hhhhhh......hhhhhhhhhhhhhhh..eee.........hhhhhhhhh.eeee...................eeehhhhhhhhh..................eeeee..hhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhh.eee..eeeeeeee.....eeeeeeeeeeee......eeeeee.....eeee..eeee......hhhhhhh.........................eee.hhhhhh..hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yry D   1 MKNRKTPMKEQSPESRRRNFEEVALGYTLEEALEEAQRCLQCPTHPCVSGCPVEIDIPGFIRKLRDGKLEESYRILKSYNNLPAVCGRVCPQEVQCESRCVVGKMKDSEPVAIGRLERFVADWAAENLEEDVKPLAGSKKEKVAVVGSGPAGLTAAADLAKMGYHVDIFEAFHKPGGVLVYGIPEFRLPKRIVEREVSYIRKLGVNFHLNTVVGKTVKVKELLSEYDAVFIGTGAGTPKFMGIPGTNLNGVYSANEFLTRVNLMKAYLFPEYDTPIRVGKKVAVIGAGNTAMDAARSALRLGAEKVYIVYRRTEREMPARREEYHHALEEGIEFLWLTLPIRYIGDANGNVEAMECVRMELKEADGSGRPRPVPIEGSNFVLEVDMVIEAIGQGPNRVLLSEFPGLELNERGYIKADEDTGATSVKGVFAGGDIVTGAATVIKAMGAGKKAAQFIHSYLTGEWNPWQK 468
                                    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

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 "SCOP Domain" information available for 4YRY)

(no "CATH Domain" information available for 4YRY)

(no "Pfam Domain" information available for 4YRY)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly A:243 - Pro A:244	[ RasMol ]
		Gly A:92 - Pro A:93	[ RasMol ]
		Gly C:243 - Pro C:244	[ RasMol ]
		Gly C:92 - Pro C:93	[ RasMol ]
		Lys B:133 - Pro B:134	[ RasMol ]
		Phe B:269 - Pro B:270	[ RasMol ]
		Phe D:269 - Pro D:270	[ RasMol ]
		Pro B:175 - Gly B:176	[ RasMol ]
		Thr B:237 - Pro B:238	[ RasMol ]
		Thr D:237 - Pro D:238	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4yry
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	Q9X1X5_THEMA \| Q9X1X5
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(no "Related Entries Specified in the PDB File" available for 4YRY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (9, 13)

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