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(-) Description

Title :  CRYSTAL STRUCTURE OF 5-FORMLY-3-HYDROXY-2-METHYLPYRIDINE 4-CARBOXYLIC ACID (FHMPC) 5-DEHYDROGENASE, AN NAD+ DEPENDENT DISMUTASE.
 
Authors :  A. N. Mugo, J. Kobayashi, B. Mikami, T. Yagi, K. Ohnishi
Date :  27 Jan 14  (Deposition) - 28 Jan 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Dehydrogenase, Dismutase, Structural Genomics, Enzyme Function Initiative, Rossmann Fold, Nad-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. N. Mugo, J. Kobayashi, B. Mikami, Y. Yoshikane, T. Yagi, K. Ohnishi
Crystal Structure Of 5-Formyl-3-Hydroxy-2-Methylpyridine 4-Carboxylic Acid 5-Dehydrogenase, An Nad(+)-Dependent Dismutase From Mesorhizobium Loti
Biochem. Biophys. Res. Commun. V. 456 35 2015
PubMed-ID: 25446130  |  Reference-DOI: 10.1016/J.BBRC.2014.11.028

(-) Compounds

Molecule 1 - 3-HYDROXYBUTYRYL-COA DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3GOL-1Ligand/IonGLYCEROL
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3GOL2Ligand/IonGLYCEROL
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:277 , CYS A:281 , GLN B:159 , THR B:160 , HOH B:688BINDING SITE FOR RESIDUE BME A 401
2AC2SOFTWAREILE A:8 , GLY A:11 , THR A:12 , MET A:13 , TYR A:31 , ASP A:32 , VAL A:33 , ALA A:37 , ASN A:86 , VAL A:87 , PRO A:88 , GLU A:89 , LYS A:94 , ASP A:114 , THR A:115 , SER A:116 , TRP A:138 , ASN A:140 , HOH A:537 , HOH A:540 , HOH A:574 , HOH A:593 , HOH A:729 , HOH A:731 , HOH A:763 , HOH A:863 , HOH A:893BINDING SITE FOR RESIDUE NAD A 402
3AC3SOFTWARESER A:116 , GLY A:117 , GLY A:184 , ASN A:188 , VAL A:244 , HOH A:572 , HOH A:828BINDING SITE FOR RESIDUE ACT A 403
4AC4SOFTWARETYR A:192 , ALA A:236BINDING SITE FOR RESIDUE ACT A 404
5AC5SOFTWAREGLY B:276 , GLU B:277 , CYS B:281BINDING SITE FOR RESIDUE BME B 401
6AC6SOFTWAREILE B:8 , GLY B:11 , THR B:12 , MET B:13 , TYR B:31 , ASP B:32 , VAL B:33 , ASN B:86 , VAL B:87 , PRO B:88 , GLU B:89 , LYS B:94 , VAL B:97 , ASP B:114 , THR B:115 , SER B:116 , HIS B:137 , TRP B:138 , ASN B:140 , HOH B:569 , HOH B:570 , HOH B:592 , HOH B:596 , HOH B:602 , HOH B:644 , HOH B:694 , HOH B:716 , HOH B:717 , HOH B:761 , HOH B:765BINDING SITE FOR RESIDUE NAD B 402
7AC7SOFTWARETYR B:192 , ALA B:236 , HOH B:647 , HOH B:774BINDING SITE FOR RESIDUE ACT B 403
8AC8SOFTWAREHOH A:640 , HOH A:808 , MET B:1 , ILE B:2 , THR B:163 , ASP B:166 , LEU B:167 , SER B:170BINDING SITE FOR RESIDUE GOL B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OM8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OM8)

(-) Exons   (0, 0)

(no "Exon" information available for 4OM8)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhh...eeee....hhhhhhhhhhhhhh......eeee.....hhhhhhhhh.hhh.eeeee.........eeeee.....hhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4om8 A   1 MIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE 309
                                    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       290       300         


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhh...eeee....hhhhhhhhhhhhhh......eeee.....hhhhhhh...hhh.eeeee.........eeeee.....hhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4om8 B   1 MIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE 309
                                    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       290       300
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4OM8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OM8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OM8)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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