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(-) Description

Title :  RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND
 
Authors :  M. E. Newcomer, A. L. Lamb
Date :  23 Jun 98  (Deposition) - 22 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Aldehyde Dehydrogenase, Retinoid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. L. Lamb, M. E. Newcomer
The Structure Of Retinal Dehydrogenase Type Ii At 2. 7 A Resolution: Implications For Retinal Specificity.
Biochemistry V. 38 6003 1999
PubMed-ID: 10320326  |  Reference-DOI: 10.1021/BI9900471
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINAL DEHYDROGENASE TYPE II
    Cellular LocationCYTOPLASM
    ChainsA, B, C, D
    EC Number1.2.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System Cell LineBL21 (DE3)
    Expression System Taxid562
    OrganTESTIS
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRALDH2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAD8Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG D:259BINDING SITE FOR RESIDUE CL C 504
2AC2SOFTWAREILE A:165 , ILE A:166 , TRP A:168 , LYS A:192 , ALA A:194 , GLU A:195 , GLY A:225 , GLY A:229 , ALA A:230 , PHE A:243 , SER A:246 , VAL A:249 , LEU A:252 , HOH A:711BINDING SITE FOR RESIDUE NAD A 701
3AC3SOFTWAREILE B:165 , ILE B:166 , TRP B:168 , LYS B:192 , ALA B:194 , GLU B:195 , GLY B:225 , GLY B:229 , ALA B:230 , PHE B:243 , SER B:246 , VAL B:249 , HOH B:738BINDING SITE FOR RESIDUE NAD B 702
4AC4SOFTWAREILE C:165 , TRP C:168 , LYS C:192 , ALA C:194 , GLU C:195 , GLN C:196 , GLY C:225 , GLY C:229 , ALA C:230 , PHE C:243 , SER C:246 , VAL C:249 , ILE C:253 , HOH C:720 , HOH C:755BINDING SITE FOR RESIDUE NAD C 703
5AC5SOFTWAREILE D:165 , ILE D:166 , TRP D:168 , LYS D:192 , ALA D:194 , GLU D:195 , GLY D:225 , GLY D:229 , ALA D:230 , PHE D:243 , SER D:246 , VAL D:249BINDING SITE FOR RESIDUE NAD D 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BI9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BI9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BI9)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.AL1A2_RAT285-292
 
 
 
  4A:267-274
B:267-274
C:267-274
D:267-274
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.AL1A2_RAT313-324
 
 
 
  4A:295-306
B:295-306
C:295-306
D:295-306
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.AL1A2_RAT285-292
 
 
 
  4A:267-274
B:267-274
C:267-274
D:267-274
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.AL1A2_RAT313-324
 
 
 
  4A:295-306
B:295-306
C:295-306
D:295-306
Biological Unit 2 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.AL1A2_RAT285-292
 
 
 
  8A:267-274
B:267-274
C:267-274
D:267-274
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.AL1A2_RAT313-324
 
 
 
  8A:295-306
B:295-306
C:295-306
D:295-306

(-) Exons   (0, 0)

(no "Exon" information available for 1BI9)

(-) 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:478
 aligned with AL1A2_RAT | Q63639 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:499
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509         
            AL1A2_RAT    20 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVTVKIPQKNS 518
               SCOP domains d1bi9a_ A: Aldehyde reductase (dehydrogenase), ALDH                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------1bi9A01 A:8-270 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                              1bi9A02 A:271-478 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                                     ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eee..eee......eeeee......eeeeee...hhhhhhhhhhhhhhh....hhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhh..............eeeeeeeee..eeeee.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh......eee.......hhhhhh......eeeeee.hhhhhhhhhhhhh....eeeeee.....eee.....hhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh....................eeee......hhhh......eeeeeee..hhhhhhhhh.......eeee...hhhhhhhhhh.....eee...---------------------...hhh..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bi9 A   2 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCY---------------------GEFGLREYSEVKTVTVKIPQKNS 500
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    |    -         -      |481       491         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                456                   478                      

Chain B from PDB  Type:PROTEIN  Length:477
 aligned with AL1A2_RAT | Q63639 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:498
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510        
            AL1A2_RAT    21 ASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVTVKIPQKNS 518
               SCOP domains d1bi9b_ B: Aldehyde reductase (dehydrogenase), ALDH                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----1bi9B01 B:8-270 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                              1bi9B02 B:271-478 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                                     ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................eee..eee......eeeee......eeeeee...hhhhhhhhhhhhhhh....hhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhh...............eeeeeeeee..eeeee.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh......eee.......hhhhhh......eeeeee.hhhhhhhhhhhhh....eeeeee.....eee.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh....................eeee......hhhh......eeee.....hhhhhhhhh.......eeee...hhhhhhhhhh.....eee...---------------------........eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bi9 B   3 ASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCY---------------------GEFGLREYSEVKTVTVKIPQKNS 500
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   |     -         -     | 482       492        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               456                   478                      

Chain C from PDB  Type:PROTEIN  Length:480
 aligned with AL1A2_RAT | Q63639 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:499
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509         
            AL1A2_RAT    20 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVTVKIPQKNS 518
               SCOP domains d1bi9c_ C: Aldehyde reductase (dehydrogenase), ALDH                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------1bi9C01 C:8-270 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                              1bi9C02 C:271-478 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                                     ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eee..eee......eeeee......eeeeee...hhhhhhhhhhhhhhh....hhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhh..............eeeeeeeee..eeeee.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh......eee.......hhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeee.....eee.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh....................eeee......hhhh......eeee.....hhhhhhhhh.......eeee...hhhhhhhhhh.....eee.....-------------------........eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bi9 C   2 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNA-------------------GEFGLREYSEVKTVTVKIPQKNS 500
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      |  -         -      |481       491         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  458                 478                      

Chain D from PDB  Type:PROTEIN  Length:482
 aligned with AL1A2_RAT | Q63639 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:499
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509         
            AL1A2_RAT    20 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVTVKIPQKNS 518
               SCOP domains d1bi9d_ D: Aldehyde reductase (dehydrogenase), ALDH                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------1bi9D01 D:8-270 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                              1bi9D02 D:271-460 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                   ---------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eee..eee......eeeee......eeeeee...hhhhhhhhhhhhhhh....hhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhh...............eeeeeeeee..eeeee.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh......eee.......hhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeee.....eee.....hhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh....................eeee......hhhh......eeeeeee..hhhhhhhhh.......eeee...hhhhhhhhhh.....eee.......-----------------.hhhhh..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bi9 D   2 MASLQLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVCNPATGEQVCEVQEADKVDIDKAVQAARLAFSLGSVWRRMDASERGRLLDKLADLVERDRATLATMESLNGGKPFLQAFYIDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFTWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVVNILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVKRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALMVSSAMQAGTVWINCYNALN-----------------GEFGLREYSEVKTVTVKIPQKNS 500
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        |-         -      |481       491         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    460               478                      

   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 Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BI9)

(-) Gene Ontology  (51, 51)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (AL1A2_RAT | Q63639)
molecular function
    GO:0004028    3-chloroallyl aldehyde dehydrogenase activity    Catalysis of the reaction: 3-chloroallyl aldehyde + H2O = 2 H+ + 2 e- + 3-chloroacrylic acid.
    GO:0004029    aldehyde dehydrogenase (NAD) activity    Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + 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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0016918    retinal binding    Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina.
    GO:0001758    retinal dehydrogenase activity    Catalysis of the reaction: retinal + NAD+ + H2O = retinoate + NADH. Acts on both 11-trans and 13-cis forms of retinal.
biological process
    GO:0042904    9-cis-retinoic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of 9-cis-retinoic acid, a metabolically active vitamin A derivative.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0048738    cardiac muscle tissue development    The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0009855    determination of bilateral symmetry    The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.
    GO:0031076    embryonic camera-type eye development    The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0035115    embryonic forelimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0060324    face development    The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0030902    hindbrain development    The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0007494    midgut development    The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
    GO:0016331    morphogenesis of embryonic epithelium    The process in which the anatomical structures of embryonic epithelia are generated and organized.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0014032    neural crest cell development    The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0021915    neural tube development    The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    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.
    GO:0031016    pancreas development    The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
    GO:0021983    pituitary gland development    The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0009954    proximal/distal pattern formation    The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end).
    GO:0001936    regulation of endothelial cell proliferation    Any process that modulates the frequency, rate, or extent of endothelial cell proliferation.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0033189    response to vitamin A    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus.
    GO:0042574    retinal metabolic process    The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A.
    GO:0002138    retinoic acid biosynthetic process    The chemical reactions and pathways resulting in the biosynthesis of retinoic acid, one of the three components that makes up vitamin A.
    GO:0042573    retinoic acid metabolic process    The chemical reactions and pathways involving retinoic acid, one of the three components that makes up vitamin A.
    GO:0048384    retinoic acid receptor signaling pathway    The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0035799    ureter maturation    A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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