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(-) Description

Title :  CRYSTAL STRUCTURE OF APE0912 FROM AEROPYRUM PERNIX K1
 
Authors :  T. Ichimura, A. Yamamura, F. Mimoto, J. Ohtsuka, K. Miyazono, M. Okai, M C. Lee, K. Nagata, M. Tanokura
Date :  10 May 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  A (1x),B (1x)
Keywords :  Dehydrogenase, Reductase, Sdr, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamamura, T. Ichimura, F. Mimoto, J. Ohtsuka, K. Miyazono, M. Okai, M. Kamo, W. -C. Lee, K. Nagata, M. Tanokura
A Unique Catalytic Triad Revealed By The Crystal Structure Of Ape0912, A Short-Chain Dehydrogenase/Reductase Family Protein From Aeropyrum Pernix K1
Proteins V. 70 1640 2008
PubMed-ID: 18175326  |  Reference-DOI: 10.1002/PROT.21860

(-) Compounds

Molecule 1 - DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1
    Synonym: SHORT-CHAIN DEHYDROGENASE/REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB
Biological Unit 4 (1x): AB
Biological Unit 5 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:87 , LYS A:134 , TRP A:136 , HOH A:2136BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWARETHR A:93 , GLY A:94 , HOH A:2020 , HOH A:2074BINDING SITE FOR RESIDUE NA A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1N)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1N)

(-) 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:237
 aligned with Q9YDK1_AERPE | Q9YDK1 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q9YDK1_AERPE     1 MDLGIQGKLAVVTAGSSGLGFASALELARNGARLLLFSRNREKLEAAASRIASLVSGAQVDIVAGDIREPGDIDRLFEKARDLGGADILVYSTGGPRPGRFMELGVEDWDESYRLLARSAVWVGRRAAEQMVEKGWGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVVRTLALELAPHGVTVNAVLPSLILTDRVRSLAEERARRSGITVEEALKSMASRIPMGRVGKPEELASVVAFLASEKASFITGAVIPVDGGAHI 260
               SCOP domains d2z1na_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2z1nA00 A:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhh...-----------------------........hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1n A   1 MDLGIQGKLAVVTAGSSGLGFASALELARNGARLLLFSRNREKLEAAASRIASLVSGAQVDIVAGDIREPGDIDRLFEKARDLGGADILVYSTGGPRPGRFMELGVEDWDESYRLLARSAVWVGRRAAEQMVEKGWGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVVRTLALELAPHGVTVNAVLPSLILTDRVR-----------------------RIPMGRVGKPEELASVVAFLASEKASFITGAVIPVDGGAHI 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     |   -         -       220       230       240       250       260
                                                                                                                                                                                                                             196                     220                                        


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q9YDK1_AERPE | Q9YDK1 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q9YDK1_AERPE     1 MDLGIQGKLAVVTAGSSGLGFASALELARNGARLLLFSRNREKLEAAASRIASLVSGAQVDIVAGDIREPGDIDRLFEKARDLGGADILVYSTGGPRPGRFMELGVEDWDESYRLLARSAVWVGRRAAEQMVEKGWGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVVRTLALELAPHGVTVNAVLPSLILTDRVRSLAEERARRSGITVEEALKSMASRIPMGRVGKPEELASVVAFLASEKASFITGAVIPVDGGAHI 260
               SCOP domains d2z1nb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2z1nB00 B:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ------------adh_short_C2-2z1nB01 B:13-259                                                                                                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) ------------adh_short_C2-2z1nB02 B:13-259                                                                                                                                                                                                                          - Pfam domains (2)
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhh-----------------............hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1n B   1 MDLGIQGKLAVVTAGSSGLGFASALELARNGARLLLFSRNREKLEAAASRIASLVSGAQVDIVAGDIREPGDIDRLFEKARDLGGADILVYSTGGPRPGRFMELGVEDWDESYRLLARSAVWVGRRAAEQMVEKGWGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVVRTLALELAPHGVTVNAVLPSLILTDRVRSL-----------------SMASRIPMGRVGKPEELASVVAFLASEKASFITGAVIPVDGGAHI 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       | -         -     | 220       230       240       250       260
                                                                                                                                                                                                                               198               216
   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, 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: NADP_Rossmann (1239)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2Z1N)

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