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(-) Description

Title :  CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE
 
Authors :  F. S. Mathews, L. W. Lim, S. White
Date :  15 Oct 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Barber, P. J. Neame, L. W. Lim, S. White, F. S. Matthews
Correlation Of X-Ray Deduced And Experimental Amino Acid Sequences Of Trimethylamine Dehydrogenase.
J. Biol. Chem. V. 267 6611 1992
PubMed-ID: 1551870
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIMETHYLAMINE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.5.99.7
    Engineered: YES
    Organism Scientific: METHYLOPHILUS METHYLOTROPHUS
    Organism Taxid: 2327
    Strain: W3A1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:322 , ILE A:325 , CYS A:345 , ILE A:346 , CYS A:348 , ASN A:349 , CYS A:351 , CYS A:364 , THR A:365BINDING SITE FOR RESIDUE SF4 A 801
2AC2SOFTWAREVAL A:27 , PRO A:28 , HIS A:29 , CYS A:30 , GLU A:59 , TYR A:60 , GLU A:103 , TYR A:169 , HIS A:172 , ARG A:222 , TRP A:264 , ASP A:267 , VAL A:297 , ARG A:299 , CYS A:320 , ALA A:321 , ARG A:322 , PRO A:323 , HOH A:811 , HOH A:865BINDING SITE FOR RESIDUE FMN A 802
3AC3SOFTWAREGLY A:396 , GLY A:398 , PRO A:399 , SER A:400 , ASP A:419 , THR A:420 , GLY A:426 , HIS A:427 , PRO A:469 , MET A:470 , ALA A:486 , THR A:487 , GLY A:488 , GLY A:673 , ASP A:674 , HOH A:804 , HOH A:848 , HOH A:911 , HOH A:1007 , HOH A:1082BINDING SITE FOR RESIDUE ADP A 803
4AC4SOFTWAREARG B:322 , ILE B:325 , CYS B:345 , ILE B:346 , GLY B:347 , CYS B:348 , ASN B:349 , CYS B:351 , CYS B:364 , THR B:365BINDING SITE FOR RESIDUE SF4 B 801
5AC5SOFTWAREVAL B:27 , PRO B:28 , HIS B:29 , CYS B:30 , GLU B:59 , TYR B:60 , GLU B:103 , TYR B:169 , HIS B:172 , ARG B:222 , TRP B:264 , ASP B:267 , ALA B:268 , VAL B:297 , ARG B:299 , CYS B:320 , ALA B:321 , ARG B:322 , PRO B:323 , ILE B:352 , HOH B:825 , HOH B:861BINDING SITE FOR RESIDUE FMN B 802
6AC6SOFTWAREGLY B:396 , GLY B:398 , PRO B:399 , SER B:400 , ASP B:419 , THR B:420 , GLY B:426 , HIS B:427 , PRO B:469 , MET B:470 , ALA B:486 , THR B:487 , GLY B:488 , ASP B:674 , HOH B:816 , HOH B:833 , HOH B:860 , HOH B:948 , HOH B:1026 , HOH B:1045BINDING SITE FOR RESIDUE ADP B 803

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:70 -His A:71
2Thr B:70 -His B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2TMD)

(-) Exons   (0, 0)

(no "Exon" information available for 2TMD)

(-) 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 A from PDB  Type:PROTEIN  Length:729
 aligned with DHTM_METME | P16099 from UniProtKB/Swiss-Prot  Length:730

    Alignment length:729
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721         
           DHTM_METME     2 ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV 730
               SCOP domains d2tmda1 A:1-340 Trimethylamine dehydrogenase, N-terminal domain                                                                                                                                                                                                                                                                                     d2tmda3 A:341-489,A:646-729 Trimethylamine dehydrogenase, middle domain                                                                              d2tmda2 A:490-645 Trimethylamine dehydrogenase, C-terminal domain                                                                                           d2tmda3 A:341-489,A:646-729 Trimethylamine dehydrogenase, middle domain              SCOP domains
               CATH domains 2tmdA01 A:1-384 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                2tmdA02 A:385-491,A:644-704 NAD(P)-binding Rossmann-like Domain                                            2tmdA03 A:492-643  [code=3.50.50.60, no name defined]                                                                                                   2tmdA02 A:385-491,A:644-704                                  ------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.............eee...........hhhhhhhhhhhhh....eeeeeeee.................hhhhhhhhhhhhhhhh...eeeeeee..hhh..............................hhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh..............hhhhhhhhhhhhhhhhhhh....eeeeeeeee............hhhhhhhhhhhh..eeeeee....hhhh............hhhhhhhhh......eee......hhhhhhhhhh.....eee..hhhh...hhhhhh...hhhh.......hhhhhhhh...............hhhh..............eeeee....hhhhhhhhhhh...eeeee.........hhhh......hhhhhhhhhhhhhhhhhh......eee.......hhhhh.....eeee............................ee.hhhhhh.......eeeeee.....hhhhhhhhhhh...eeeeee......hhhh...hhhhhhhhhh...eeee.eeeeeee..eeeeee........................eeee..eeeee.......hhhhhhhh...........eeee.........hhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tmd A   1 ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV 729
                                    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       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720         


Chain B from PDB  Type:PROTEIN  Length:729
 aligned with DHTM_METME | P16099 from UniProtKB/Swiss-Prot  Length:730

    Alignment length:729
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721         
           DHTM_METME     2 ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV 730
               SCOP domains d2tmdb1 B:1-340 Trimethylamine dehydrogenase, N-terminal domain                                                                                                                                                                                                                                                                                     d2tmdb3 B:341-489,B:646-729 Trimethylamine dehydrogenase, middle domain                                                                              d2tmdb2 B:490-645 Trimethylamine dehydrogenase, C-terminal domain                                                                                           d2tmdb3 B:341-489,B:646-729 Trimethylamine dehydrogenase, middle domain              SCOP domains
               CATH domains 2tmdB01 B:1-384 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                2tmdB02 B:385-491,B:644-704 NAD(P)-binding Rossmann-like Domain                                            2tmdB03 B:492-643  [code=3.50.50.60, no name defined]                                                                                                   2tmdB02 B:385-491,B:644-704                                  ------------------------- CATH domains
           Pfam domains (1) -------Oxidored_FMN-2tmdB03 B:8-341                                                                                                                                                                                                                                                                                                                  -------------------------------------------------Pyr_redox_2-2tmdB01 B:391-534                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------Oxidored_FMN-2tmdB04 B:8-341                                                                                                                                                                                                                                                                                                                  -------------------------------------------------Pyr_redox_2-2tmdB02 B:391-534                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhh.............eee...........hhhhhhhhhhhhh....eeeeeeee.................hhhhhhhhhhhhhhhh...eeeeeee..hhh..............................hhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh..............hhhhhhhhhhhhhhhhhhh....eeeeeeeee............hhhhhhhhhhhh..eeeeee....hhhh............hhhhhhhhh......eee......hhhhhhhhhh.....eee..hhhh...hhhhhh...hhhh.......hhhhhhhh...............hhhh..............eeeee....hhhhhhhhhhh...eeeee.........hhhh......hhhhhhhhhhhhhhhhhh......eee.......hhhhh.....eeee............................ee.hhhhhh.......eeeeee.....hhhhhhhhhhh...eeeeee......hhhh...hhhhhhhhhh...eeee.eeeeeee..eeeeee........................eeee..eeeee.......hhhhhhhh...........eeee.........hhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tmd B   1 ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV 729
                                    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       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHTM_METME | P16099)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0050470    trimethylamine dehydrogenase activity    Catalysis of the reaction: trimethylamine + H2O + electron-transferring flavoprotein = dimethylamine + formaldehyde + reduced electron-transferring flavoprotein.
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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        DHTM_METME | P16099: 1djn 1djq 1o94 1o95

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