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(-) Description

Title :  THE CLOSED FORM OF SERINE DEHYDROGENASE COMPLEXED WITH NADP+
 
Authors :  R. Yamazawa, Y. Nakajima, T. Yoshimoto, K. Ito
Date :  21 Dec 10  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Sdr Family, Rossmann Fold, Short-Chain Dehydrogenase/Reductase, L- Allo-Threonine Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Yamazawa, Y. Nakajima, K. Mushiake, T. Yoshimoto, K. Ito
Crystal Structure Of Serine Dehydrogenase From Escherichia Coli: Important Role Of The C-Terminal Region For Closed-Complex Formation.
J. Biochem. V. 149 701 2011
PubMed-ID: 21349860  |  Reference-DOI: 10.1093/JB/MVR024

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECDH1_2106, YDFG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: XL1-BLUE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): AB    
Biological Unit 2 (1x):   CDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1NAP6Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:7 , THR A:9 , ALA A:10 , GLY A:11 , PHE A:12 , GLY A:31 , ARG A:32 , ARG A:33 , LEU A:53 , ASP A:54 , VAL A:55 , ARG A:56 , ASN A:81 , ALA A:82 , GLY A:83 , ILE A:132 , GLY A:133 , SER A:134 , TYR A:147 , LYS A:151 , PRO A:177 , GLY A:178 , VAL A:180 , THR A:183 , GLU A:184 , PHE A:185 , PO4 A:311 , HOH A:1011 , HOH A:1097 , HOH A:1186 , HOH A:1243 , HOH A:1254 , HOH A:1278 , HOH A:1315BINDING SITE FOR RESIDUE NAP A 301
02AC2SOFTWARESER A:134 , THR A:135 , ALA A:136 , TYR A:141 , TYR A:147 , GLY A:178 , PHE A:185 , NAP A:301BINDING SITE FOR RESIDUE PO4 A 311
03AC3SOFTWAREGLY B:7 , THR B:9 , ALA B:10 , GLY B:11 , PHE B:12 , ARG B:32 , ARG B:33 , LEU B:53 , ASP B:54 , VAL B:55 , ARG B:56 , ASN B:81 , ALA B:82 , GLY B:83 , ILE B:132 , GLY B:133 , SER B:134 , TYR B:147 , LYS B:151 , PRO B:177 , GLY B:178 , VAL B:180 , THR B:183 , GLU B:184 , PHE B:185 , PO4 B:312 , HOH B:1111 , HOH B:1182BINDING SITE FOR RESIDUE NAP B 302
04AC4SOFTWARESER B:134 , ALA B:136 , TYR B:141 , TYR B:147 , GLY B:178 , PHE B:185 , NAP B:302 , HOH B:1087BINDING SITE FOR RESIDUE PO4 B 312
05AC5SOFTWAREGLY C:7 , THR C:9 , ALA C:10 , GLY C:11 , PHE C:12 , ARG C:32 , ARG C:33 , LEU C:53 , ASP C:54 , VAL C:55 , ARG C:56 , ASN C:81 , ALA C:82 , GLY C:83 , THR C:105 , ILE C:132 , GLY C:133 , SER C:134 , TYR C:147 , LYS C:151 , PRO C:177 , GLY C:178 , VAL C:180 , THR C:183 , GLU C:184 , PHE C:185 , PO4 C:313 , HOH C:1009 , HOH C:1017 , HOH C:1322BINDING SITE FOR RESIDUE NAP C 303
06AC6SOFTWARESER C:134 , TYR C:141 , TYR C:147 , GLY C:178 , PHE C:185 , NAP C:303BINDING SITE FOR RESIDUE PO4 C 313
07AC7SOFTWAREGLY D:7 , THR D:9 , ALA D:10 , GLY D:11 , PHE D:12 , ARG D:32 , ARG D:33 , LEU D:53 , ASP D:54 , VAL D:55 , ARG D:56 , ASN D:81 , ALA D:82 , GLY D:83 , ILE D:132 , GLY D:133 , SER D:134 , TYR D:147 , LYS D:151 , PRO D:177 , GLY D:178 , VAL D:180 , THR D:183 , GLU D:184 , PHE D:185 , PO4 D:314 , HOH D:1109 , HOH D:1114 , HOH D:1207BINDING SITE FOR RESIDUE NAP D 304
08AC8SOFTWARESER D:134 , TYR D:141 , TYR D:147 , GLY D:178 , PHE D:185 , NAP D:304BINDING SITE FOR RESIDUE PO4 D 314
09AC9SOFTWAREGLY E:7 , THR E:9 , ALA E:10 , GLY E:11 , PHE E:12 , ARG E:32 , ARG E:33 , LEU E:53 , ASP E:54 , VAL E:55 , ARG E:56 , ASN E:81 , GLY E:83 , THR E:105 , ILE E:132 , GLY E:133 , TYR E:147 , LYS E:151 , PRO E:177 , GLY E:178 , VAL E:180 , THR E:183 , GLU E:184 , PHE E:185 , PO4 E:315 , HOH E:1197 , HOH E:1271BINDING SITE FOR RESIDUE NAP E 305
10BC1SOFTWARESER E:134 , ALA E:136 , TYR E:141 , TYR E:147 , GLY E:178 , PHE E:185 , ARG E:189 , NAP E:305BINDING SITE FOR RESIDUE PO4 E 315
11BC2SOFTWAREGLY F:7 , THR F:9 , ALA F:10 , GLY F:11 , PHE F:12 , ARG F:32 , ARG F:33 , LEU F:53 , ASP F:54 , VAL F:55 , ARG F:56 , ASN F:81 , ALA F:82 , GLY F:83 , THR F:105 , ILE F:132 , GLY F:133 , SER F:134 , TYR F:147 , LYS F:151 , PRO F:177 , GLY F:178 , VAL F:180 , THR F:183 , GLU F:184 , PHE F:185 , PO4 F:316 , HOH F:1026 , HOH F:1119 , HOH F:1142BINDING SITE FOR RESIDUE NAP F 306
12BC3SOFTWARESER F:134 , THR F:135 , ALA F:136 , TYR F:141 , TYR F:147 , GLY F:178 , PHE F:185 , NAP F:306BINDING SITE FOR RESIDUE PO4 F 316

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ASV)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asva_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh........eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh........eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv A   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asvb_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh........eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv B   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asvc_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeeeee..eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv C   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        


Chain D from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asvd_ D: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhh.hhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhh....eeeeeeeeee..eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv D   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        


Chain E from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asve_ E: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.hhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeeeee..eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv E   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        


Chain F from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d3asvf_ F: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeeeee..eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asv F   1 MIVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQELKDELGDNLYIAQLDVRNRAAIEEMLASLPAEWCNIDILVNNAGLALGMEPAHKASVEDWETMIDTNNKGLVYMTRAVLPGMVERNHGHIINIGSTAGSWPYAGGNVYGATKAFVRQFSLNLRTDLHGTAVRVTDIEPGLVGGTEFSNVRFKGDDGKAEKTYQNTVALTPEDVSEAVWWVSTLPAHVNINTLEMMPVTQSYAGLNVHRQ 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
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  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, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ASV)

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3asu THE SAME ENZYME