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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION
 
Authors :  G. S. Prasad, V. Sridhar, M. Yamaguchi, Y. Hatefi, C. D. Stout
Date :  04 Oct 99  (Deposition) - 20 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide-Binding Fold, Protein-Nadp(H) Complex, Inverted Binding Of Nadp(H), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. S. Prasad, V. Sridhar, M. Yamaguchi, Y. Hatefi, C. D. Stout
Crystal Structure Of Transhydrogenase Domain Iii At 1. 2 A Resolution.
Nat. Struct. Biol. V. 6 1126 1999
PubMed-ID: 10581554  |  Reference-DOI: 10.1038/70067
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADP(H) TRANSHYDROGENASE
    Cellular LocationMITOCHONDRIA
    ChainsA
    EC Number1.6.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentNADP(H) BINDING DOMAIN
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:23 , GLY A:30 , TYR A:31 , GLY A:32 , ALA A:35 , ALA A:36 , VAL A:63 , ALA A:64 , GLY A:65 , ARG A:66 , MET A:67 , PRO A:68 , GLY A:105 , ALA A:106 , ASN A:107 , ASP A:108 , THR A:109 , LYS A:140 , ARG A:141 , SER A:142 , VAL A:145 , GLY A:146 , TYR A:147 , ASP A:166 , ALA A:167 , HOH A:314 , HOH A:326 , HOH A:353 , HOH A:357 , HOH A:366 , HOH A:442BINDING SITE FOR RESIDUE NAP A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D4O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D4O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D4O)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSBTAT000000157691aENSBTAE00000128321chr20:33185168-33184964205NNTM_BOVIN1-51510--
1.2ENSBTAT000000157692ENSBTAE00000128327chr20:33178970-33178741230NNTM_BOVIN51-127770--
1.3ENSBTAT000000157693ENSBTAE00000128331chr20:33175581-33175364218NNTM_BOVIN128-200730--
1.4ENSBTAT000000157694ENSBTAE00000128333chr20:33171055-3317096888NNTM_BOVIN200-229300--
1.5ENSBTAT000000157695ENSBTAE00000128335chr20:33166499-3316641189NNTM_BOVIN230-259300--
1.6ENSBTAT000000157696ENSBTAE00000128337chr20:33163276-33163089188NNTM_BOVIN259-322640--
1.7ENSBTAT000000157697ENSBTAE00000128339chr20:33145052-33144919134NNTM_BOVIN322-366450--
1.8ENSBTAT000000157698ENSBTAE00000128341chr20:33144647-33144456192NNTM_BOVIN367-430640--
1.9ENSBTAT000000157699ENSBTAE00000128343chr20:33143472-33143319154NNTM_BOVIN431-482520--
1.10ENSBTAT0000001576910ENSBTAE00000128344chr20:33140351-33140190162NNTM_BOVIN482-536550--
1.11ENSBTAT0000001576911ENSBTAE00000128345chr20:33139115-33139005111NNTM_BOVIN536-573380--
1.12ENSBTAT0000001576912ENSBTAE00000128346chr20:33138058-33137913146NNTM_BOVIN573-621490--
1.13ENSBTAT0000001576913ENSBTAE00000128347chr20:33136683-33136488196NNTM_BOVIN622-687660--
1.14ENSBTAT0000001576914ENSBTAE00000128348chr20:33133045-33132812234NNTM_BOVIN687-765790--
1.15ENSBTAT0000001576915ENSBTAE00000128349chr20:33131707-33131547161NNTM_BOVIN765-818540--
1.16ENSBTAT0000001576916ENSBTAE00000128350chr20:33129981-33129802180NNTM_BOVIN819-878600--
1.17ENSBTAT0000001576917ENSBTAE00000128351chr20:33122899-33122740160NNTM_BOVIN879-932541A:5-3026
1.18ENSBTAT0000001576918ENSBTAE00000287971chr20:33120337-3312025682NNTM_BOVIN932-959281A:30-5728
1.19ENSBTAT0000001576919ENSBTAE00000128353chr20:33102801-33102683119NNTM_BOVIN959-999411A:57-9741
1.20ENSBTAT0000001576920ENSBTAE00000128354chr20:33101215-33101100116NNTM_BOVIN999-1037391A:97-13539
1.21bENSBTAT0000001576921bENSBTAE00000128355chr20:33099105-33098561545NNTM_BOVIN1038-1086491A:136-18146

(-) 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:177
 aligned with NNTM_BOVIN | P11024 from UniProtKB/Swiss-Prot  Length:1086

    Alignment length:177
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076       
          NNTM_BOVIN    907 GTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLSEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES 1083
               SCOP domains d1d4oa_ A: Transhydrogenase domain III (dIII)                                                                                                                                     SCOP domains
               CATH domains 1d4oA00 A:5-181 TPP-binding domain                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.eeeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhh.hhh.eeehhhhhhhhhhh.eeeee..hhhhhhhhhhh...........hhhhh..eeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.17  PDB: A:5-30    --------------------------Exon 1.19  PDB: A:57-97 UniProt: 959-999 --------------------------------------Exon 1.21b  PDB: A:136-181 UniProt: 1038-1086  Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.18  PDB: A:30-57     ---------------------------------------Exon 1.20  PDB: A:97-135               ---------------------------------------------- Transcript 1 (2)
                1d4o A    5 GTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLSEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES  181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D4O)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NNTM_BOVIN | P11024)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0008746    NAD(P)+ transhydrogenase activity    Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+.
    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:0006740    NADPH regeneration    A metabolic process that generates a pool of NADPH by the reduction of NADP+.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
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:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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