3CLU - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE R236K MUTANT FROM METHYLOPHILUS METHYLOTROPHUS ETF

Authors :   G. Katona, D. Leys

Date :   20 Mar 08 (Deposition) - 08 Apr 08 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : C,D

Keywords :   Etf, Tmadh, Electron Transfer, Flavoprotein, Dynamic Interface, Electron Transport, Fad, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Burgess, H. L. Messiha, G. Katona, S. E. Rigby, D. Leys, N. S. Scrutton
Probing The Dynamic Interface Between Trimethylamine Dehydrogenase (Tmadh) And Electron Transferring Flavoprotei (Etf) In The Tmadh-2Etf Complex: Role Of The Arg-Alpha237 (Etf) And Tyr-442 (Tmadh) Residue Pair.
Biochemistry V. 47 5168 2008
PubMed-ID: 18407658 | Reference-DOI: 10.1021/BI800127D

Molecule 1 - ELECTRON TRANSFER FLAVOPROTEIN SUBUNIT BETA
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ETFB
	Organism Scientific	:	METHYLOPHILUS METHYLOTROPHUS
	Organism Taxid	:	17
	Synonym	:	BETA-ETF, ELECTRON TRANSFER FLAVOPROTEIN SMALL SUBUNIT, ETFSS

Molecule 2 - ELECTRON TRANSFER FLAVOPROTEIN SUBUNIT ALPHA
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ETFA
	Mutation	:	YES
	Organism Scientific	:	METHYLOPHILUS METHYLOTROPHUS
	Organism Taxid	:	17
	Synonym	:	ALPHA-ETF, ELECTRON TRANSFER FLAVOPROTEIN LARGE SUBUNIT, ETFLS

		1	2
Asymmetric/Biological Unit	:	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA C:6 , LYS C:8 , ASN C:36 , ASP C:39 , SER C:63 , ALA C:118 , GLY C:119 , GLN C:121 , SER C:122 , TYR C:127 , ALA C:128 , SER C:129 , THR C:130	BINDING SITE FOR RESIDUE AMP C 1262
2	AC2	SOFTWARE	GLN C:121 , GLN C:183 , LEU C:184 , GLY D:209 , ARG D:210 , GLY D:211 , SER D:235 , LYS D:236 , PRO D:237 , GLN D:249 , GLY D:251 , GLN D:252 , SER D:253 , GLY D:254 , GLY D:267 , ILE D:268 , SER D:269 , SER D:271 , GLN D:273 , HIS D:274 , ASN D:288 , THR D:289 , ASP D:290 , ALA D:305 , ASP D:306 , ILE D:307	BINDING SITE FOR RESIDUE FAD D 1319

(no "SS Bond" information available for 3CLU)

Asymmetric/Biological Unit

No.	Residues
1	Cys C:176	-	Pro C:177

(no "SAP(SNP)/Variant" information available for 3CLU)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_METME	160-181	1	C:160-181
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_METME	263-289	1	D:262-288

(no "Exon" information available for 3CLU)

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 C from PDB  Type:PROTEIN  Length:252
 aligned with ETFB_METME | P53570 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:261
                                    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 
           ETFB_METME     1 MKILVAVKQTAALEEDFEIREDGMDVDEDFMMYDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYKPGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYASLRGIKQAATKPIEEVSLADIGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEF 261
               SCOP domains d3cluc_ C: Small, beta subunit of electron transfer flavoprotein ETFP                                                                                                                                                                                                 SCOP domains
               CATH domains 3cluC00 C:1-261 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee.............hhh.eeeeehhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhh...eeeee.hhhhh..hhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhh..eeeeeeeee......eeeeeee.....eeeeeee...eeee...........---------...eee.hhhhh.hhhhhhhhhh..eeeeee.......ee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA              -------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clu C   1 MKILVAVKQTAALEEDFEIREDGMDVDEDFMMYDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYKPGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYAS---------KPIEEVSLADIGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEF 261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  |      -  |    210       220       230       240       250       260 
                                                                                                                                                                                                                          193       203

Chain D from PDB  Type:PROTEIN  Length:319
 aligned with ETFA_METME | P53571 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
           ETFA_METME     2 SKILVIAEHRRNDLRPVSLELIGAANGLKKSGEDKVVVAVIGSQADAFVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHSVDSLGYASSLASKTGYGFATDVYIVEYQGDELVATRGGYNQKVNVEVDFPGKSTVVLTIRPSVFKPLEGAGSPVVSNVDAPSVQSRSQNKDYVEVGGGNDIDITTVDFIMSIGRGIGEETNVEQFRELADEAGATLCCSRPIADAGWLPKSRQVGQSGKVVGSCKLYVAMGISGSIQHMAGMKHVPTIIAVNTDPGASIFTIAKYGIVADIFDIEEELKAQLA 320
               SCOP domains d3clud1 D:1-191 Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain                                                                                                 d3clud2 D:192-319 C-terminal domain of the electron transfer flavoprotein alpha subunit                                          SCOP domains
               CATH domains 3cluD01 D:1-188 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                       3cluD02 D:189-319 TPP-binding domain                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..ee..ee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh.eeeeee.eeeee..eeeeeeee....eeeeee......eeeee..............eeeeee.......eeeeeee........hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhh...hhhhh............eeeee....hhhhhh......eeeee.....hhhhhh..eee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: D:262-288  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clu D   1 SKILVIAEHRRNDLRPVSLELIGAANGLKKSGEDKVVVAVIGSQADAFVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHSVDSLGYASSLASKTGYGFATDVYIVEYQGDELVATRGGYNQKVNVEVDFPGKSTVVLTIRPSVFKPLEGAGSPVVSNVDAPSVQSRSQNKDYVEVGGGNDIDITTVDFIMSIGRGIGEETNVEQFRELADEAGATLCCSKPIADAGWLPKSRQVGQSGKVVGSCKLYVAMGISGSIQHMAGMKHVPTIIAVNTDPGASIFTIAKYGIVADIFDIEEELKAQLA 319
                                    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

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Methylophilus methylotrophus. Organism_taxid: 17. (4)

3cluD02

D:189-319

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Methylophilus methylotrophus. Organism_taxid: 17. (4)

2a	3cluD01	D:1-188
2b	3cluC00	C:1-261

(no "Pfam Domain" information available for 3CLU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C (ETFB_METME | P53570)

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.
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.

Chain D (ETFA_METME | P53571)

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:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
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.

Asymmetric/Biological Unit
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Cys C:176 - Pro C:177	[ RasMol ]

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	ETFB_METME \| P53570
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1o97	WT PROTEIN
3clr	R236A ETF
3cls	R236C ETF
3clt	R236E ETF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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