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(-) Description

Title :  CRYSTAL STRUCTURE OF R. RUBRUM TRANSHYDROGENASE DOMAIN III BOUND TO NADPH
 
Authors :  V. Sundaresan, M. Yamaguchi, J. Chartron, C. D. Stout
Date :  12 Jun 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleotide Binding Fold, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Sundaresan, M. Yamaguchi, J. Chartron, C. D. Stout
Conformational Change In The Nadp(H) Binding Domain Of Transhydrogenase Defines Four States
Biochemistry V. 42 12143 2003
PubMed-ID: 14567675  |  Reference-DOI: 10.1021/BI035006Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAD(P) TRANSHYDROGENASE SUBUNIT BETA
    Chains: A, B
    EC Number: 1.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Organism Taxid: 1085
    Synonym: PYRIDINE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT BETA, NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT BETA, PROTON-TRANSLOCATING TRANSHYDROGENASE NADP(H)-BINDING COMPONENT, DIII

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:5 , HOH A:7 , HOH A:9 , HOH A:24 , HOH A:146 , GLY A:315 , TYR A:316 , GLY A:317 , VAL A:348 , ALA A:349 , GLY A:350 , ARG A:351 , MET A:352 , PRO A:353 , GLY A:390 , ALA A:391 , ASN A:392 , ASP A:393 , VAL A:394 , PRO A:406 , ILE A:407 , LYS A:425 , ARG A:426 , SER A:427 , ALA A:429 , SER A:430 , GLY A:431 , TYR A:432 , ASP A:451 , ALA A:452BINDING SITE FOR RESIDUE NDP A 500
2AC2SOFTWAREHOH B:113 , GLY B:315 , TYR B:316 , GLY B:317 , VAL B:348 , ALA B:349 , GLY B:350 , ARG B:351 , MET B:352 , PRO B:353 , GLY B:390 , ALA B:391 , ASN B:392 , ASP B:393 , VAL B:394 , LYS B:425 , ARG B:426 , SER B:427 , ALA B:429 , SER B:430 , GLY B:431 , TYR B:432 , GLY B:450 , ASP B:451 , ALA B:452BINDING SITE FOR RESIDUE NDP B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PNQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PNQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PNQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PNQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1PNQ)

(-) Sequences/Alignments

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:180
 aligned with PNTB_RHORT | Q2RSB4 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:182
                                   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  
           PNTB_RHORT   283 AGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
               SCOP domains d1pnqa  _ A: Transhydrogenase domain III (dIII)                                                                                                                                        SCOP domains
               CATH domains 1pnqA0  0 A:285-464 TPP-binding domain                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.--.eee.hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eee.hhhhhhhh...eeeee......hhhhh...................eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnq A 285 SGHIEG--RHMAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
                                 | 292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  
                               290  |                                                                                                                                                                             
                                  291                                                                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:180
 aligned with PNTB_RHORU | P0C188 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:182
                                   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  
           PNTB_RHORU   283 AGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
               SCOP domains d1pnqa  _ A: Transhydrogenase domain III (dIII)                                                                                                                                        SCOP domains
               CATH domains 1pnqA0  0 A:285-464 TPP-binding domain                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.--.eee.hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eee.hhhhhhhh...eeeee......hhhhh...................eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnq A 285 SGHIEG--RHMAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
                                 | 292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  
                               290  |                                                                                                                                                                             
                                  291                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PNTB_RHORT | Q2RSB4 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:189
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
           PNTB_RHORT   276 SEGGVAAAGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
               SCOP domains d1p            nqb_ B: Transhydrogenase domain III (dIII)                                                                                                                                     SCOP domains
               CATH domains 1pn            qB00 B:288-464 TPP-binding domain                                                                                                                                              CATH domains
           Pfam domains (1) ------------------PNTB-1pnqB01 B:294-463                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) ------------------PNTB-1pnqB02 B:294-463                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ...------------..ee.hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eee...hhhhhhhh.eeeee..hhhhhhhhh.............hhhhh.eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnq B 288 IEG------------RHMAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
                              |      -     | 295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
                            290          291                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PNTB_RHORU | P0C188 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:189
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
           PNTB_RHORU   276 SEGGVAAAGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
               SCOP domains d1p            nqb_ B: Transhydrogenase domain III (dIII)                                                                                                                                     SCOP domains
               CATH domains 1pn            qB00 B:288-464 TPP-binding domain                                                                                                                                              CATH domains
           Pfam domains (1) ------------------PNTB-1pnqB01 B:294-463                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) ------------------PNTB-1pnqB02 B:294-463                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ...------------..ee.hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eee...hhhhhhhh.eeeee..hhhhhhhhh.............hhhhh.eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnq B 288 IEG------------RHMAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN 464
                              |      -     | 295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
                            290          291
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: FAD_DHS (82)
(-)
Family: PNTB (11)
(-)
Rhodospirillum rubrum (9)
1aPNTB-1pnqB01B:294-463
1bPNTB-1pnqB02B:294-463

(-) Gene Ontology  (8, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PNTB_RHORU | P0C188)
molecular function
    GO:0008750    NAD(P)+ transhydrogenase (AB-specific) activity    Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD+ and B-specific (i.e. the pro-S hydrogen is transferred) with respect to NADP+.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (PNTB_RHORT | Q2RSB4)
molecular function
    GO:0008750    NAD(P)+ transhydrogenase (AB-specific) activity    Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD+ and B-specific (i.e. the pro-S hydrogen is transferred) with respect to NADP+.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  PNTB_RHORU | P0C188
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 Related Entries

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

UniProtKB/Swiss-Prot
        PNTB_RHORT | Q2RSB4: 1e3t 1hzz 1nm5 1pno 1ptj 1u28 1u2d 1u2g 1xlt 2fr8 2frd 2fsv
        PNTB_RHORU | P0C188: 1e3t 1hzz 1nm5 1pno 1ptj 1u28 1u2d 1u2g 1xlt 2fr8 2frd 2fsv 2oo5 2oor

(-) Related Entries Specified in the PDB File

1pno THE SAME PROTEIN BOUND TO NADP