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(-) Description

Title :  CRYSTAL STRUCTURE OF NADP BOUND L-SERINE 3-DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON PYROBACULUM CALIDIFONTIS
 
Authors :  K. Yoneda, H. Sakuraba, T. Ohshima
Date :  22 Feb 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hyperthermophilic Archaeon, Rossmann Fold, L-Serine 3-Dehydrogenase, Nad(P) Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yoneda, H. Sakuraba, T. Ohshima
Crystal Structure Of Nadp Bound L-Serine 3-Dehydrogenase From Hyperthermophilic Archaeon Pyrobaculum Calidifontis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, NAD-BINDING PROTEIN
    Chains: A
    EC Number: 1.1.1.276
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PCAL_0699
    Organism Scientific: PYROBACULUM CALIDIFONTIS
    Organism Taxid: 410359
    Strain: JCM 11548 / VA1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (2, 26)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , LEU A:8 , GLY A:9 , ILE A:10 , MSE A:11 , ASN A:30 , ARG A:31 , THR A:32 , LYS A:35 , VAL A:64 , SER A:65 , ASP A:69 , SER A:94 , THR A:95 , VAL A:120 , GLY A:123 , GLY A:230 , PHE A:231 , LYS A:232 , HIS A:235 , LYS A:238 , HOH A:403 , HOH A:409 , HOH A:411 , HOH A:414 , HOH A:435BINDING SITE FOR RESIDUE NAP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W6U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:229 -Gly A:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W6U)

(-) Exons   (0, 0)

(no "Exon" information available for 3W6U)

(-) 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:279
 aligned with A3MU08_PYRCJ | A3MU08 from UniProtKB/TrEMBL  Length:286

    Alignment length:283
                                    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   
         A3MU08_PYRCJ     1 MRVGFIGLGIMGGPMATHLLKAGFLAAVYNRTREKTKPFAEAGVYVAESPADLAKRVDVVIVMVSDAPDVEQVLFGPSGVVEGARPGLIVVDMSTNSPDWARKFAERLAQYGIEFLDAPVTGGQKGAIEGTLTIMVGGKEELFHRLLPIFKAMGRDIVYMGPVGYGQAMKLVNQVVVALNTVAMVEGLKLAKALGLDMDKVAEVLTRGAARSGAIELYLPKLLKGDLSPGFKAEHLKKDLGYVLEEARKRGVKLPGAELAYELYRKMVEDGAGSLGIHALGFY 283
               SCOP domains d3w6ua1 A:1-161 automated matches                                                                                                                                d3w6ua2 A:162-283 automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhh...ee..hhhhhhh...eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhh..eeeeee.hhhhhhhhhhhhhhheeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh----.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w6u A   1 mRVGFIGLGImGGPmATHLLKAGFLAAVYNRTREKTKPFAEAGVYVAESPADLAKRVDVVIVmVSDAPDVEQVLFGPSGVVEGARPGLIVVDmSTNSPDWARKFAERLAQYGIEFLDAPVTGGQKGAIEGTLTImVGGKEELFHRLLPIFKAmGRDIVYmGPVGYGQAmKLVNQVVVALNTVAmVEGLKLAKALGLDmDKVAEVLT----RSGAIELYLPKLLKGDLSPGFKAEHLKKDLGYVLEEARKRGVKLPGAELAYELYRKmVEDGAGSLGIHALGFY 283
                            |       10|   |   20        30        40        50        60  |     70        80        90  |    100       110       120       130    |  140       150  |    160       170       180   |   190       200     |   -|      220       230       240       250       260      |270       280   
                            |        11-MSE                                              63-MSE                        93-MSE                                   135-MSE           153-MSE  |      169-MSE        184-MSE       198-MSE 206  211                                                     267-MSE            
                            1-MSE        15-MSE                                                                                                                                          160-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W6U)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (A3MU08_PYRCJ | A3MU08)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
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

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        A3MU08_PYRCJ | A3MU08: 3w6z 3ws7

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