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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHORT-CHAIN DEHYDROGENASE GALACTITOL-DEHYDROGENASE (GATDH) OF RHODOBACTER SPHAEROIDES IN COMPLEX WITH NAD
 
Authors :  Y. Carius, H. Christian, A. Faust, P. Kornberger, G. W. Kohring, F. Giffhorn, A. J. Scheidig
Date :  04 Sep 09  (Deposition) - 28 Apr 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Sdr, Rossmann Fold, Tagatose (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
    Atcc: 17023
    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: 469008
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: D

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3POL8Ligand/IonN-PROPANOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:254 , HOH A:2465 , HOH A:2467 , TRP B:254 , HOH B:2413 , HOH B:2414BINDING SITE FOR RESIDUE MG A 256
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 , ALA A:93 , GLY A:94 , VAL A:115 , 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 , MET A:196 , THR A:197 , POL A:1256 , HOH A:2158 , HOH A:2298 , HOH A:2300 , HOH A:2368 , HOH A:2469BINDING SITE FOR RESIDUE NAD A 500
03AC3SOFTWAREGLY B:18 , SER 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 , LEU B:142 , GLY B:143 , SER B:144 , TYR B:159 , LYS B:163 , PRO B:189 , GLY B:190 , VAL B:192 , THR B:194 , GLU B:195 , MET B:196 , THR B:197 , POL B:1255 , HOH B:2036 , HOH B:2137 , HOH B:2141 , HOH B:2192 , HOH B:2241 , HOH B:2243 , HOH B:2416 , HOH B:2417BINDING SITE FOR RESIDUE NAD B 500
04AC4SOFTWARETRP C:254 , HOH C:2452 , HOH C:2453 , TRP D:254 , HOH D:2418 , HOH D:2420BINDING SITE FOR RESIDUE MG C 256
05AC5SOFTWAREGLY C:18 , SER C:21 , GLY C:22 , ILE C:23 , ASP C:42 , ARG C:43 , GLU C:44 , ALA C:65 , ASP C:66 , VAL C:67 , SER C:92 , ALA C:93 , VAL C:115 , LEU C:142 , GLY C:143 , SER C:144 , TYR C:159 , LYS C:163 , PRO C:189 , GLY C:190 , TYR C:191 , VAL C:192 , THR C:194 , MET C:196 , THR C:197 , POL C:1255 , HOH C:2101 , HOH C:2126 , HOH C:2128 , HOH C:2136 , HOH C:2265 , HOH C:2266 , HOH C:2311 , HOH C:2456BINDING SITE FOR RESIDUE NAD C 500
06AC6SOFTWAREGLY D:18 , SER 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 , VAL D:115 , LEU D:142 , GLY D:143 , SER D:144 , TYR D:159 , LYS D:163 , PRO D:189 , GLY D:190 , VAL D:192 , THR D:194 , MET D:196 , THR D:197 , POL D:1256 , HOH D:2038 , HOH D:2128 , HOH D:2246 , HOH D:2247 , HOH D:2249 , HOH D:2421 , HOH D:2423BINDING SITE FOR RESIDUE NAD D 500
07AC7SOFTWARESER C:144 , MET C:145 , SER C:146 , ASN C:151 , TYR C:159 , NAD C:500 , POL C:1256BINDING SITE FOR RESIDUE POL C1255
08AC8SOFTWAREASN A:151 , GLN A:154 , TYR A:159BINDING SITE FOR RESIDUE POL A1255
09AC9SOFTWARESER B:144 , SER B:146 , ASN B:151 , TYR B:159 , TYR B:191 , MET B:196 , THR B:197 , NAD B:500 , POL B:1256BINDING SITE FOR RESIDUE POL B1255
10BC1SOFTWAREASN B:151 , GLN B:154 , MET B:160 , MET B:200 , POL B:1255BINDING SITE FOR RESIDUE POL B1256
11BC2SOFTWARELEU D:98 , GLN D:154 , TYR D:159BINDING SITE FOR RESIDUE POL D1255
12BC3SOFTWAREALA C:96 , ASN C:151 , GLN C:154 , TYR C:159 , POL C:1255BINDING SITE FOR RESIDUE POL C1256
13BC4SOFTWARESER A:144 , SER A:146 , ASN A:151 , TYR A:159 , TYR A:191 , NAD A:500BINDING SITE FOR RESIDUE POL A1256
14BC5SOFTWARESER D:144 , SER D:146 , ASN D:151 , TYR D:159 , NAD D:500BINDING SITE FOR RESIDUE POL D1256

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:152 -Pro A:153
2Arg B:152 -Pro B:153
3Arg C:152 -Pro C:153
4Arg D:152 -Pro D:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WSB)

(-) 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsb 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsb 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsb 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------adh_short_C2-2wsbD01 D:18-252                                                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -----------------adh_short_C2-2wsbD02 D:18-252                                                                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) -----------------adh_short_C2-2wsbD03 D:18-252                                                                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) -----------------adh_short_C2-2wsbD04 D:18-252                                                                                                                                                                                                              -- Pfam domains (4)
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsb 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  (0, 0)

(no "SCOP Domain" information available for 2WSB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WSB)

(-) 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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 Related Entries

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        C0KTJ6_RHOSH | C0KTJ6: 2wdz 3lqf

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