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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SHORT CHAIN DEHYDROGENASE FROM RHODOBACTER SPHAEROIDES
 
Authors :  Z. Zhang, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar, J R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swaminathan, New Y Structural Genomics Research Consortium (Nysgrc)
Date :  05 Dec 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  A,D  (1x)
Biol. Unit 4:  B,D  (1x)
Biol. Unit 5:  B,C  (1x)
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. C. Almo, S. Swaminathan
The Crystal Structure Of Short Chain Dehydrogenase From Rhodobacter Sphaeroides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RHOS4_38900, RSP_4006
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x): A  D
Biological Unit 4 (1x):  B D
Biological Unit 5 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 5 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:13 , ALA C:15 , GLY C:16 , GLY C:17 , ILE C:18 , ASP C:37 , ARG C:38 , ASP C:52 , LEU C:53 , ARG C:54 , ASN C:79 , ALA C:80 , GLY C:81 , ILE C:83 , VAL C:102 , VAL C:129 , ALA C:130 , SER C:131 , TYR C:144 , LYS C:148 , PRO C:174 , ASN C:175 , GLU C:176 , VAL C:177 , THR C:179 , PRO C:180 , MSE C:181 , HOH C:252 , HOH C:274 , HOH C:431BINDING SITE FOR RESIDUE NAD C 245

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg C:189 -Gly C:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UXY)

(-) 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:241
 aligned with Q3IVH6_RHOS4 | Q3IVH6 from UniProtKB/TrEMBL  Length:244

    Alignment length:241
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
         Q3IVH6_RHOS4     4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLMAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCMGMDHAPQGIRINAVCPNEVNTPMLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
               SCOP domains d3uxya_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhh..eeee...........ee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uxy A   4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLmAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCmGmDHAPQGIRINAVCPNEVNTPmLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153    | |163       173       183       193       203       213       223       233       243 
                                                                                                                                            118-MSE                                 158-MSE                181-MSE                                                           
                                                                                                                                                                                      160-MSE                                                                                


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q3IVH6_RHOS4 | Q3IVH6 from UniProtKB/TrEMBL  Length:244

    Alignment length:243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   
         Q3IVH6_RHOS4     2 QGFEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLMAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCMGMDHAPQGIRINAVCPNEVNTPMLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
               SCOP domains d3uxyb_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeee...........ee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uxy B   2 QGFEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLmAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCmGmDHAPQGIRINAVCPNEVNTPmLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
                                    11        21        31        41        51        61        71        81        91       101       111      |121       131       141       151      |161       171       181       191       201       211       221       231       241   
                                                                                                                                              118-MSE                                 158-MSE                181-MSE                                                           
                                                                                                                                                                                        160-MSE                                                                                


Chain C from PDB  Type:PROTEIN  Length:241
 aligned with Q3IVH6_RHOS4 | Q3IVH6 from UniProtKB/TrEMBL  Length:244

    Alignment length:241
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
         Q3IVH6_RHOS4     4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLMAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCMGMDHAPQGIRINAVCPNEVNTPMLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
               SCOP domains d3uxyc_ C: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhh..eeee...........ee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh...hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uxy C   4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLmAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCmGmDHAPQGIRINAVCPNEVNTPmLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153    | |163       173       183       193       203       213       223       233       243 
                                                                                                                                            118-MSE                                 158-MSE                181-MSE                                                           
                                                                                                                                                                                      160-MSE                                                                                


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with Q3IVH6_RHOS4 | Q3IVH6 from UniProtKB/TrEMBL  Length:244

    Alignment length:241
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
         Q3IVH6_RHOS4     4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLMAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCMGMDHAPQGIRINAVCPNEVNTPMLRTGFAKRGFDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
               SCOP domains d3uxyd_ D: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhh..eeeeee.........eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh...---.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uxy D   4 FEGKVALVTGAAGGIGGAVVTALRAAGARVAVADRAVAGIAADLHLPGDLREAAYADGLPGAVAAGLGRLDIVVNNAGVISRGRITETTDADWSLSLGVNVEAPFRICRAAIPLmAAAGGGAIVNVASCWGLRPGPGHALYCLTKAALASLTQCmGmDHAPQGIRINAVCPNEVNTPmLRTGFA---FDPDRAVAELGRTVPLGRIAEPEDIADVVLFLASDAARYLCGSLVEVNGGKAVA 244
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153    | |163       173       183   |   193       203       213       223       233       243 
                                                                                                                                            118-MSE                                 158-MSE                181-MSE87 191                                                     
                                                                                                                                                                                      160-MSE
   Legend:   → Mismatch (orange background)
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    → 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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UXY)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q3IVH6_RHOS4 | Q3IVH6)
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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