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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHORT-CHAIN DEHYDROGENASE GALACTITOL-DEHYDROGENASE (GATDH) OF RHODOBACTER SPHAEROIDES IN COMPLEX WITH NAD AND ERYTHRITOL
 
Authors :  Y. Carius, H. Christian, A. Faust, P. Kornberger, U. Zander, B. U. Klink G. W. Kohring, F. Giffhorn, A. J. Scheidig
Date :  09 Feb 10  (Deposition) - 21 Apr 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Sdr, Rossmann Fold, Tagatose, Galactitol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Carius, H. Christian, A. Faust, U. Zander, B. U. Klink, P. Kornberger, G. W. Kohring, F. Giffhorn, A. J. Scheidig
Structural Insight Into Substrate Differentiation Of The Sugar-Metabolizing Enzyme Galactitol Dehydrogenase From Rhodobacter Sphaeroides D.
J. Biol. Chem. V. 285 20006 2010
PubMed-ID: 20410293  |  Reference-DOI: 10.1074/JBC.M110.113738

(-) Compounds

Molecule 1 - GALACTITOL DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MRY4Ligand/IonMESO-ERYTHRITOL
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:254 , HOH A:317 , HOH A:336 , HOH A:344 , TRP B:254 , HOH B:301BINDING SITE FOR RESIDUE MG A 255
02AC2SOFTWAREGLY A:18 , SER A:21 , GLY A:22 , ILE A:23 , ASP A:42 , ARG A:43 , ALA A:65 , ASP A:66 , VAL A:67 , SER A:92 , LEU A:142 , GLY A:143 , SER A:144 , TYR A:159 , LYS A:163 , PRO A:189 , GLY A:190 , VAL A:192 , THR A:194 , GLU A:195 , MET A:196 , THR A:197 , MRY A:258 , HOH A:324 , HOH A:334 , HOH A:424 , HOH A:436BINDING SITE FOR RESIDUE NAD A 257
03AC3SOFTWAREALA A:96 , ASN A:151 , GLN A:154 , TYR A:191 , THR A:197 , MET A:200 , NAD A:257 , HOH A:436BINDING SITE FOR RESIDUE MRY A 258
04AC4SOFTWARESER B:21 , GLY B:22 , ILE B:23 , ASP B:42 , ARG B:43 , GLU B:44 , ALA B:65 , ASP B:66 , VAL B:67 , SER B:92 , ALA B:93 , GLY B:94 , LEU B:142 , GLY B:143 , SER B:144 , TYR B:159 , LYS B:163 , GLY B:190 , VAL B:192 , THR B:194 , MET B:196 , THR B:197 , MRY B:258 , HOH B:319 , HOH B:371 , HOH B:399 , HOH B:419BINDING SITE FOR RESIDUE NAD B 257
05AC5SOFTWAREALA B:96 , LEU B:98 , GLN B:154 , TYR B:159 , TYR B:191 , NAD B:257BINDING SITE FOR RESIDUE MRY B 258
06AC6SOFTWARETRP C:254 , HOH C:339 , TRP D:254 , HOH D:307 , HOH D:327 , HOH D:339BINDING SITE FOR RESIDUE MG C 255
07AC7SOFTWARESER C:21 , GLY C:22 , ILE C:23 , ASP C:42 , ARG C:43 , ALA C:65 , ASP C:66 , VAL C:67 , SER C:92 , GLY C:94 , LEU C:142 , GLY C:143 , SER C:144 , TYR C:159 , LYS C:163 , PRO C:189 , GLY C:190 , VAL C:192 , THR C:194 , MET C:196 , THR C:197 , MRY C:258 , HOH C:360 , HOH C:369 , HOH C:415 , HOH C:416BINDING SITE FOR RESIDUE NAD C 257
08AC8SOFTWAREGLN C:154 , TYR C:159 , MET C:196 , THR C:197 , MET C:200 , NAD C:257 , HOH C:416BINDING SITE FOR RESIDUE MRY C 258
09AC9SOFTWARESER D:21 , GLY D:22 , ILE D:23 , ASP D:42 , ARG D:43 , ALA D:65 , ASP D:66 , VAL D:67 , SER D:92 , ALA D:93 , GLY D:94 , LEU D:142 , GLY D:143 , SER D:144 , TYR D:159 , LYS D:163 , GLY D:190 , VAL D:192 , THR D:194 , MET D:196 , THR D:197 , MRY D:258 , HOH D:326 , HOH D:363BINDING SITE FOR RESIDUE NAD D 257
10BC1SOFTWAREGLN D:154 , NAD D:257BINDING SITE FOR RESIDUE MRY D 258

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Arg A:152 -Pro A:153
2Arg B:152 -Pro B:153
3Arg C:152 -Pro C:153
4Arg C:201 -Glu C:202
5Met D:1 -Asp D:2
6Ala D:45 -Ala D:46
7Ala D:46 -Ala D:47
8Arg D:152 -Pro D:153
9Arg D:201 -Glu D:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LQF)

(-) 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:254
 aligned with C0KTJ6_RHOSH | C0KTJ6 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         C0KTJ6_RHOSH     1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
               SCOP domains d3lqfa_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqf A   1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
                                    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    


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with C0KTJ6_RHOSH | C0KTJ6 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         C0KTJ6_RHOSH     1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
               SCOP domains d3lqfb_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqf B   1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
                                    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    


Chain C from PDB  Type:PROTEIN  Length:254
 aligned with C0KTJ6_RHOSH | C0KTJ6 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         C0KTJ6_RHOSH     1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
               SCOP domains d3lqfc_ C: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqf C   1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
                                    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    


Chain D from PDB  Type:PROTEIN  Length:254
 aligned with C0KTJ6_RHOSH | C0KTJ6 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         C0KTJ6_RHOSH     1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
               SCOP domains d3lqfd_ D: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------adh_short_C2-3lqfD01 D:18-252                                                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -----------------adh_short_C2-3lqfD02 D:18-252                                                                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) -----------------adh_short_C2-3lqfD03 D:18-252                                                                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) -----------------adh_short_C2-3lqfD04 D:18-252                                                                                                                                                                                                              -- Pfam domains (4)
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqf D   1 MDYRTVFRLDGACAAVTGAGSGIGLEICRAFAASGARLILIDREAAALDRAAQELGAAVAARIVADVTDAEAMTAAAAEAEAVAPVSILVNSAGIARLHDALETDDATWRQVMAVNVDGMFWASRAFGRAMVARGAGAIVNLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAAEWAGRGVRVNALAPGYVATEMTLKMRERPELFETWLDMTPMGRCGEPSEIAAAALFLASPAASYVTGAILAVDGGYTVW 254
                                    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
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (C0KTJ6_RHOSH | C0KTJ6)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  Cis Peptide Bonds
    Ala D:45 - Ala D:46   [ RasMol ]  
    Ala D:46 - Ala D:47   [ RasMol ]  
    Arg A:152 - Pro A:153   [ RasMol ]  
    Arg B:152 - Pro B:153   [ RasMol ]  
    Arg C:152 - Pro C:153   [ RasMol ]  
    Arg C:201 - Glu C:202   [ RasMol ]  
    Arg D:152 - Pro D:153   [ RasMol ]  
    Arg D:201 - Glu D:202   [ RasMol ]  
    Met D:1 - Asp D:2   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        C0KTJ6_RHOSH | C0KTJ6: 2wdz 2wsb

(-) Related Entries Specified in the PDB File

2wdz THE SAME PROTEIN COMPLEXED WITH 1,2-S-PENTANEDIOL
2wsb THE SAME PROTEIN WITHOUT BOUND SUBSTRATE