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(-) Description

Title :  CRYSTAL STRUCTURE OF THE R236C MUTANT OF ETF FROM METHYLOPHILUS METHYLOTROPHUS
 
Authors :  G. Katona, D. Leys
Date :  20 Mar 08  (Deposition) - 08 Apr 08  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  C,D
Keywords :  Etf, Tmadh, Electron Transfer, Dynamic Interface, Electron Transport, Fad, Flavoprotein, 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

(-) Compounds

Molecule 1 - ELECTRON TRANSFER FLAVOPROTEIN SUBUNIT BETA
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneETFB
    MutationYES
    Organism ScientificMETHYLOPHILUS METHYLOTROPHUS
    Organism Taxid17
    SynonymBETA-ETF, ELECTRON TRANSFER FLAVOPROTEIN SMALL SUBUNIT, ETFSS
 
Molecule 2 - ELECTRON TRANSFER FLAVOPROTEIN SUBUNIT ALPHA
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneETFA
    Organism ScientificMETHYLOPHILUS METHYLOTROPHUS
    Organism Taxid17
    SynonymALPHA-ETF, ELECTRON TRANSFER FLAVOPROTEIN LARGE SUBUNIT, ETFLS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA 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:130BINDING SITE FOR RESIDUE AMP C 1262
2AC2SOFTWARETRP C:38 , GLN C:121 , GLN C:183 , LEU C:184 , GLY D:209 , ARG D:210 , GLY D:211 , SER D:235 , CYS 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:307BINDING SITE FOR RESIDUE FAD D 1319

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys C:176 -Pro C:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETF_BETAPS01065 Electron transfer flavoprotein beta-subunit signature.ETFB_METME160-181  1C:160-181
2ETF_ALPHAPS00696 Electron transfer flavoprotein alpha-subunit signature.ETFA_METME263-289  1D:262-288

(-) Exons   (0, 0)

(no "Exon" information available for 3CLS)

(-) Sequences/Alignments

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:254
 aligned with ETFB_METME | P53570 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:262
                                    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 MKILVAVKQTAALEEDFEIREDGMDVDEDFMMYDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYKPGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYASLRGIKQAATKPIEEVSLADIGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEFK 262
               SCOP domains d3clsc_ C: Small, beta subunit of electron transfer flavoprotein ETFP                                                                                                                                                                                                  SCOP domains
               CATH domains 3clsC00 C:1-262 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......eeeeeeee...eeeeeeee...eeee...........--------....eee.hhhhh.hhhhhhhhhh..eeeeee.......ee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA              --------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cls C   1 MKILVAVKQTAALEEDFEIREDGMDVDEDFMMYDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYKPGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYAS--------TKPIEEVSLADIGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEFK 262
                                    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      202                                                            

Chain D from PDB  Type:PROTEIN  Length:318
 aligned with ETFA_METME | P53571 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:318
                                    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 SKILVIAEHRRNDLRPVSLELIGAANGLKKSGEDKVVVAVIGSQADAFVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHSVDSLGYASSLASKTGYGFATDVYIVEYQGDELVATRGGYNQKVNVEVDFPGKSTVVLTIRPSVFKPLEGAGSPVVSNVDAPSVQSRSQNKDYVEVGGGNDIDITTVDFIMSIGRGIGEETNVEQFRELADEAGATLCCSRPIADAGWLPKSRQVGQSGKVVGSCKLYVAMGISGSIQHMAGMKHVPTIIAVNTDPGASIFTIAKYGIVADIFDIEEELKAQL 319
               SCOP domains d3clsd1 D:1-191 Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain                                                                                                 d3clsd2 D:192-318 C-terminal domain of the electron transfer flavoprotein alpha subunit                                         SCOP domains
               CATH domains 3clsD01 D:1-188 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                       3clsD02 D:189-318 TPP-binding domain                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..ee..ee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeee.eeeee..eeeeeeee....eeeeee......eeeee..............eeeeee.......eeeeeee..............eeeee.hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhh...hhhhh............eeeee....hhhhhhhhh...eeeee.....hhhhhh..eee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: D:262-288  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cls D   1 SKILVIAEHRRNDLRPVSLELIGAANGLKKSGEDKVVVAVIGSQADAFVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHSVDSLGYASSLASKTGYGFATDVYIVEYQGDELVATRGGYNQKVNVEVDFPGKSTVVLTIRPSVFKPLEGAGSPVVSNVDAPSVQSRSQNKDYVEVGGGNDIDITTVDFIMSIGRGIGEETNVEQFRELADEAGATLCCSCPIADAGWLPKSRQVGQSGKVVGSCKLYVAMGISGSIQHMAGMKHVPTIIAVNTDPGASIFTIAKYGIVADIFDIEEELKAQL 318
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 5)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ETFA_METME | P535711e11 1o94 1o95 1o96 1o97 3clr 3clt 3clu
        ETFB_METME | P535701e11 1o94 1o95 1o96 1o97 3clr 3clt 3clu

(-) Related Entries Specified in the PDB File

1o97 WT PROTEIN
3clr R236A ETF
3clt R236E ETF
3clu R236K ETF