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(-) Description

Title :  SUBSTRATE FINGERPRINT AND THE STRUCTURE OF NADP+ DEPENDENT SERINE DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH NADP+
 
Authors :  R. Huether, C. M. Pacheco, W. L. Duax
Date :  18 Apr 11  (Deposition) - 01 Jun 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Substrate Fingerprint, Short Chain Oxidoreductase, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Huether, C. M. Pacheco, W. L. Duax
Substrate Fingerprint And The Structure Of Nadp+ Dependent Serine Dehydrogenase From Saccharomyces Cerevisiae Complexe With Nadp+
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE YMR226C
    Chains: A, B, C, D
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YM9959.08C, YMR226C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: NADP+ DEPENDENT SERINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , SER A:22 , ALA A:23 , GLY A:24 , ILE A:25 , ALA A:47 , ARG A:48 , ARG A:49 , LEU A:74 , ASP A:75 , ILE A:76 , ASN A:102 , ALA A:103 , GLY A:104 , LYS A:105 , GLY A:154 , SER A:155 , TYR A:168 , LYS A:172 , PRO A:198 , GLY A:199 , VAL A:201 , THR A:203 , GLU A:204 , PHE A:205 , HOH A:274 , HOH A:296 , HOH A:297 , HOH A:303 , HOH A:330 , HOH A:331 , HOH A:348 , HOH A:551 , HOH A:555BINDING SITE FOR RESIDUE NAP A 268
2AC2SOFTWAREGLY B:20 , SER B:22 , ALA B:23 , GLY B:24 , ILE B:25 , ALA B:47 , ARG B:48 , ARG B:49 , LEU B:74 , ASP B:75 , ILE B:76 , ASN B:102 , ALA B:103 , GLY B:104 , LYS B:105 , LEU B:153 , GLY B:154 , SER B:155 , TYR B:168 , LYS B:172 , PRO B:198 , GLY B:199 , VAL B:201 , THR B:203 , GLU B:204 , PHE B:205 , HOH B:275 , HOH B:277 , HOH B:290 , HOH B:291 , HOH B:319 , HOH B:334 , HOH B:417 , HOH B:554BINDING SITE FOR RESIDUE NAP B 268
3AC3SOFTWAREGLY C:20 , SER C:22 , ALA C:23 , GLY C:24 , ILE C:25 , ALA C:47 , ARG C:48 , ARG C:49 , LEU C:74 , ASP C:75 , ILE C:76 , ASN C:102 , ALA C:103 , GLY C:104 , LYS C:105 , LEU C:153 , GLY C:154 , TYR C:168 , LYS C:172 , PRO C:198 , GLY C:199 , VAL C:201 , THR C:203 , GLU C:204 , PHE C:205 , HOH C:269 , HOH C:274 , HOH C:279 , HOH C:284 , HOH C:296 , HOH C:351 , HOH C:419 , HOH C:544BINDING SITE FOR RESIDUE NAP C 268
4AC4SOFTWAREGLY D:20 , SER D:22 , ALA D:23 , GLY D:24 , ILE D:25 , ALA D:47 , ARG D:48 , ARG D:49 , LEU D:74 , ASP D:75 , ILE D:76 , ASN D:102 , ALA D:103 , GLY D:104 , LYS D:105 , LEU D:153 , GLY D:154 , TYR D:168 , LYS D:172 , PRO D:198 , GLY D:199 , VAL D:201 , THR D:203 , GLU D:204 , PHE D:205 , HOH D:269 , HOH D:271 , HOH D:273 , HOH D:283 , HOH D:285 , HOH D:297 , HOH D:336 , HOH D:375 , HOH D:553BINDING SITE FOR RESIDUE NAP D 268

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RKU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.YM71_YEAST155-183
 
 
 		  4A:155-183
B:155-183
C:155-183
D:155-183

(-) Exons   (0, 0)

(no "Exon" information available for 3RKU)

(-) 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:268
 aligned with YM71_YEAST | Q05016 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:268
                             1                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           YM71_YEAST     - -MSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
               SCOP domains d3rkua_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.hhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..ee.hhhhhhh..hhhhhhhhhh....eehhhhhhhhhhhhh....eeeeeeeeee..eee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:155-183    ------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rku A   0 HMSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with YM71_YEAST | Q05016 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:268
                             1                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           YM71_YEAST     - -MSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
               SCOP domains d3rkub_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.hhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..ee.hhhhhhh..hhhhhhhhhh....eehhhhhhhhhhhhh....eeeeeeeeee..eee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:155-183    ------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rku B   0 HMSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        


Chain C from PDB  Type:PROTEIN  Length:268
 aligned with YM71_YEAST | Q05016 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:268
                             1                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           YM71_YEAST     - -MSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
               SCOP domains d3rkuc_ C: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeee...hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.hhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..ee.hhhhhhh..hhhhhhhhhh....eehhhhhhhhhhhhh....eeeeeeeeee..eee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:155-183    ------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rku C   0 HMSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        


Chain D from PDB  Type:PROTEIN  Length:268
 aligned with YM71_YEAST | Q05016 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:268
                             1                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           YM71_YEAST     - -MSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
               SCOP domains d3rkud_ D: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------adh_short-3rkuD01 D:14-187                                                                                                                                                    -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------adh_short-3rkuD02 D:14-187                                                                                                                                                    -------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------adh_short-3rkuD03 D:14-187                                                                                                                                                    -------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------adh_short-3rkuD04 D:14-187                                                                                                                                                    -------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ....hhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.hhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..ee.hhhhhhh..hhhhhhhhhh....eehhhhhhhhhhhhh....eeeeeeeeee..eee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:155-183    ------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rku D   0 HMSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARRLEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDILVNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGDIVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPGLVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIADTLIFPTNQASPHHIFRG 267
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (YM71_YEAST | Q05016)
molecular function
    GO:0004090    carbonyl reductase (NADPH) activity    Catalysis of the reaction: R-CHOH-R' + NADP+ = R-CO-R' + NADPH + H+.
    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:0031132    serine 3-dehydrogenase activity    Catalysis of the reaction: L-serine + NADP(+) = L-alpha-formylglycine + 2 H(+) + NADPH.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3rku
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 Related Entries

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