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(-) Description

Title :  2.00 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF NAD- AND SUBSTRATE-BOUND 2-AMINOMUCONATE 6-SEMIALDEHYDE DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS
 
Authors :  L. Huo, I. Davis, L. Chen, A. Liu
Date :  21 Nov 12  (Deposition) - 21 May 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldehyde Dehydrogenase, Dehydrogenase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Huo, I. Davis, F. Liu, B. Andi, S. Esaki, H. Iwaki, Y. Hasegawa, A. M. Orville, A. Liu
Crystallographic And Spectroscopic Snapshots Reveal A Dehydrogenase In Action.
Nat Commun V. 6 5935 2015
PubMed-ID: 25565451  |  Reference-DOI: 10.1038/NCOMMS6935

(-) Compounds

Molecule 1 - 2-AMINOMUCONATE 6-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16BB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NBAE
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Strain: KU-7

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
16OD4Ligand/Ion(2E,4E)-2-AMINO-6-OXOHEXA-2,4-DIENOIC ACID
2NA4Ligand/IonSODIUM ION
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:165 , SER A:166 , PRO A:167 , TRP A:168 , ASN A:169 , LYS A:192 , SER A:194 , GLU A:195 , PHE A:224 , GLY A:225 , GLY A:230 , GLU A:231 , PHE A:244 , THR A:245 , GLY A:246 , GLU A:247 , THR A:250 , GLU A:268 , LEU A:269 , GLY A:270 , CYS A:302 , GLU A:404 , PHE A:406 , 6OD A:603 , HOH A:848 , HOH A:866 , HOH A:1004 , HOH A:1030BINDING SITE FOR RESIDUE NAD A 601
02AC2SOFTWAREASN A:37 , ILE A:38 , ASP A:105 , GLU A:196 , HOH A:746 , HOH A:1029BINDING SITE FOR RESIDUE NA A 602
03AC3SOFTWAREARG A:120 , LEU A:174 , TRP A:177 , CYS A:302 , TYR A:462 , ARG A:464 , PHE A:470 , NAD A:601BINDING SITE FOR RESIDUE 6OD A 603
04AC4SOFTWAREASN B:37 , ILE B:38 , ASP B:105 , GLU B:196 , HOH B:741 , HOH B:789BINDING SITE FOR RESIDUE NA B 601
05AC5SOFTWAREARG B:120 , LEU B:174 , TRP B:177 , GLU B:268 , CYS B:302 , TYR B:462 , ARG B:464 , PHE B:470 , NAD B:603BINDING SITE FOR RESIDUE 6OD B 602
06AC6SOFTWAREILE B:165 , SER B:166 , PRO B:167 , TRP B:168 , ASN B:169 , LYS B:192 , SER B:194 , GLU B:195 , PHE B:224 , GLY B:225 , GLY B:230 , GLU B:231 , PHE B:244 , THR B:245 , GLY B:246 , GLU B:247 , THR B:250 , THR B:253 , GLU B:268 , LEU B:269 , GLY B:270 , CYS B:302 , GLU B:404 , PHE B:406 , PHE B:470 , 6OD B:602 , HOH B:858 , HOH B:970BINDING SITE FOR RESIDUE NAD B 603
07AC7SOFTWAREILE C:165 , SER C:166 , PRO C:167 , TRP C:168 , ASN C:169 , LEU C:174 , LYS C:192 , SER C:194 , GLU C:195 , PHE C:224 , GLY C:225 , GLY C:230 , GLU C:231 , PHE C:244 , THR C:245 , GLY C:246 , GLU C:247 , THR C:250 , GLU C:268 , LEU C:269 , GLY C:270 , CYS C:302 , GLU C:404 , PHE C:406 , PHE C:470 , 6OD C:603 , HOH C:924 , HOH C:981BINDING SITE FOR RESIDUE NAD C 601
08AC8SOFTWAREASN C:37 , ILE C:38 , ASP C:105 , GLU C:196 , HOH C:765 , HOH C:797BINDING SITE FOR RESIDUE NA C 602
09AC9SOFTWAREARG C:120 , LEU C:174 , GLU C:268 , CYS C:302 , TYR C:462 , ARG C:464 , PHE C:470 , NAD C:601BINDING SITE FOR RESIDUE 6OD C 603
10BC1SOFTWAREILE D:165 , SER D:166 , PRO D:167 , TRP D:168 , ASN D:169 , LEU D:174 , LYS D:192 , SER D:194 , GLU D:195 , PHE D:224 , GLY D:225 , GLY D:230 , GLU D:231 , PHE D:244 , THR D:245 , GLY D:246 , GLU D:247 , THR D:250 , GLU D:268 , LEU D:269 , GLY D:270 , CYS D:302 , GLU D:404 , PHE D:406 , PHE D:470 , 6OD D:603 , HOH D:727 , HOH D:867 , HOH D:900 , HOH D:998 , HOH D:1056 , HOH D:1062BINDING SITE FOR RESIDUE NAD D 601
11BC2SOFTWAREASN D:37 , ILE D:38 , ASP D:105 , GLU D:196 , HOH D:757 , HOH D:794BINDING SITE FOR RESIDUE NA D 602
12BC3SOFTWAREARG D:120 , LEU D:174 , GLU D:268 , CYS D:302 , TYR D:462 , ARG D:464 , PHE D:470 , NAD D:601BINDING SITE FOR RESIDUE 6OD D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I25)

(-) Exons   (0, 0)

(no "Exon" information available for 4I25)

(-) 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:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..eee...eeeeee......eeeeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee.......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.....eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh..ee.eeeee..hhhhhhhhhh.....eeee..............ee..ee...hhhhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i25 A  18 SQLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497   


Chain B from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eeeeee......eeeeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eee.......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.....eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh..ee.eeeee..hhhhhhhhhh.....eeee..............ee..ee...hhhhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i25 B  18 SQLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497   


Chain C from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..eee...eeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee.......hhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.....eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhh.....eeee..............hhh.ee...hhhhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i25 C  18 SQLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497   


Chain D from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..eee...eeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee.......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.....eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhh.....eeee..............hhh.ee....hhhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i25 D  18 SQLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
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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 4I25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I25)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q83V33_PSEFL | Q83V33: 4i1w 4i26 4i2r 4npi 4oe2 4ou2 4oub 5kj5 5klk 5kll 5klm 5kln 5klo

(-) Related Entries Specified in the PDB File

4i1w 4i26 4i2r