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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS TRANSHYDROGENASE HETEROTRIMERIC COMPLEX OF THE ALPHA1 SUBUNIT DIMER WITH THE NADP BINDING DOMAIN (DOMAIN III) OF THE BETA SUBUNIT
 
Authors :  M. Yamaguchi, J. Leung, L. A. Schurig Briccio, R. B. Gennis, C. D. Stout
Date :  01 Feb 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Soluble Components Of Nicotinamide Nucleotide Transhydrogenase, Complex Of Alpha1 Subunit Dimer With Domain Iii Of Beta Subunit, Alpha1 Binds Nad(H), Domain Iii Binds Nadp(H), Domain Iii Binds To Alpha1, Nad Bound To Alpha1, Nadp Bound To Domain Iii, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yamaguchi, J. Leung, L. A. Schurig Briccio, R. B. Gennis, C. D. Stou
Crystal Structure Analysis Of Thermus Thermophilus Transhydrogenase Soluble Domains
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAD/NADP TRANSHYDROGENASE ALPHA SUBUNIT 1
    Chains: A, B
    EC Number: 1.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3) ACRAB-
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TT_C1780
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27 / ATCC BAA-163 / DSM 7039
 
Molecule 2 - NAD(P) TRANSHYDROGENASE SUBUNIT BETA
    Chains: C
    EC Number: 1.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3) ACRAB-
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DOMAIN III (UNP RESIDUES 266-450)
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27 / ATCC BAA-163 / DSM 7039
    Synonym: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT BETA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:122 , GLY A:174 , VAL A:175 , GLY A:176 , ASP A:197 , ARG A:199 , ARG A:228 , GLN A:257 , LEU A:266 , HOH A:601BINDING SITE FOR RESIDUE NAD A 500
2AC2SOFTWAREARG B:122 , ILE B:123 , THR B:124 , GLN B:127 , SER B:133 , GLY B:174 , VAL B:175 , GLY B:176 , VAL B:177 , TYR B:196 , ASP B:197 , VAL B:198 , ARG B:199 , GLN B:238 , ALA B:256 , GLN B:257 , PRO B:264BINDING SITE FOR RESIDUE NAD B 401
3AC3SOFTWAREHOH A:621 , HIS B:146 , ARG B:149BINDING SITE FOR RESIDUE CL B 402
4AC4SOFTWAREARG B:122 , LEU B:132 , PRO B:259BINDING SITE FOR RESIDUE PGE B 403
5AC5SOFTWAREARG A:188 , LYS B:187 , ARG B:188 , GLY B:190 , VAL C:343 , ALA C:346 , GLU C:347BINDING SITE FOR RESIDUE GOL B 404
6AC6SOFTWAREGLN A:127 , GLY C:300 , TYR C:301 , GLY C:302 , LEU C:305 , SER C:306 , VAL C:333 , ALA C:334 , GLY C:335 , ARG C:336 , MET C:337 , PRO C:338 , GLY C:375 , ALA C:376 , ASN C:377 , ASP C:378 , VAL C:379 , LYS C:409 , ARG C:410 , GLY C:411 , GLN C:412 , GLY C:413 , GLY C:415 , PHE C:416 , GLY C:434 , ASP C:435 , ALA C:436 , HOH C:617 , HOH C:625 , HOH C:626BINDING SITE FOR RESIDUE NAP C 501
7AC7SOFTWAREMET A:157 , MET C:288 , TYR C:291 , ALA C:292 , ASP C:369 , ASN C:404BINDING SITE FOR RESIDUE GOL C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J16)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu B:216 -Pro B:217
2Glu B:221 -Gly B:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J16)

(-) Exons   (0, 0)

(no "Exon" information available for 4J16)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee...hhhhh.hhhhhhh...eee..........eee.....hhhhhhhh....eeee......hhhhhhhhhhh..eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee..eee...eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhh...ee........hhhhh....hhhhhhhhhhhhhhhhhh..eeee.............hhhhhh......eeee.hhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhh...ee..ee.....hhhhhhheeee..ee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j16 A   1 MVTVAVPKERAPGERRVALVPEVVARLVKGGARVRVERGAGEGAYHPDEAYQEAGAEVVERGELLKGAHLLFTVQPPPEDLIQALEPGAIVVGFVQPHKNLELVRALQAKKATVIAMELIPRITRAQSMDALSSQATVAGYLAAIHAARLSPRFFPMLTTAAGTIRPAKVMVMGVGVAGLMAIATAKRLGAQVFAYDVRKAALEQALSLGAKPIELPISAEGEGGYARELTEEEKRIQHEALRDHVAGMDVLITTAQVPGRRAPILLTEDMVERLKPGTVVVDLAAESGGNCVLTKPGEVVEVRGVRVYGPLNLPSELSVHASEMYAKNLYNLSSLLIEKGAFAPKWEDEIVRAALLMKEGEVLHGPTKALL 372
                                    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  


Chain B from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee.........hhhhhhhh..eeehhhhh.....eee.....hhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee.hhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhh......eee..eee...eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.................hhhhhhhhhhhh....eeee.............hhhhhh......eeee.hhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhh..ee..ee.....hhhhhhheeee..ee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j16 B   1 MVTVAVPKERAPGERRVALVPEVVARLVKGGARVRVERGAGEGAYHPDEAYQEAGAEVVERGELLKGAHLLFTVQPPPEDLIQALEPGAIVVGFVQPHKNLELVRALQAKKATVIAMELIPRITRAQSMDALSSQATVAGYLAAIHAARLSPRFFPMLTTAAGTIRPAKVMVMGVGVAGLMAIATAKRLGAQVFAYDVRKAALEQALSLGAKPIELPISAEGARELTEEEKRIQHEALRDHVAGMDVLITTAQVPGRRAPILLTEDMVERLKPGTVVVDLAAESGGNCVLTKPGEVVEVRGVRVYGPLNLPSELSVHASEMYAKNLYNLSSLLIEKGAFAPKWEDEIVRAALLMKEGEVLHGPTKALLG 373
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 ||    234       244       254       264       274       284       294       304       314       324       334       344       354       364         
                                                                                                                                                                                                                                                       222|                                                                                                                                                  
                                                                                                                                                                                                                                                        227                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains d4j16c_ C: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh..eeeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhh.hhh.eeehhhhhhhhhhh.eeeee..hhhhhhhhhh...........hhhhh..eeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j16 C 274 KGSLKPIDVEDAAVMLAYAGKVVFVPGYGMALSQAQHKLKELADLLEARGVEVKFAIHPVAGRMPGHMNVLLAEAGVDYDKLKDLEEINPEFPTVDVAVVIGANDVVNPAARRPGSPLYGMPILDVDKAKNVIVIKRGQGKGFAGVENELFYAENTRMLYGDAQKVLTELIQALKRL 450
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J16)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J16)

(-) Gene Ontology  (8, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:221 - Gly B:222   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q72GS0_THET2 | Q72GS0: 5uni
UniProtKB/TrEMBL
        Q72GR8_THET2 | Q72GR8: 4izh 4izi 4j1t 4o9u
        Q72GS0_THET2 | Q72GS0: 4j1t 4o93 4o9p 4o9t 4o9u

(-) Related Entries Specified in the PDB File

1xlt CRYSTAL STRUCTURE OF R. RUBRUM TRANSHYDROGENASE [(DOMAIN I) 2:DOMAIN III] HETEROTRIMER COMPLEX
4j1t CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS TRANSHYDROGENASE HETEROTRIMERIC COMPLEX OF THE ALPHA1 SUBUNIT DIMER WITH THE NADP BINDING DOMAIN (DOMAIN III) OF THE BETA SUBUNIT IN P2(1)