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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROBABLE SORBITOL DEHYDROGENASE (TARGET PSI-012078) FROM SINORHIZOBIUM MELILOTI 1021
 
Authors :  P. R. Kumar, S. C. Almo, New York Structural Genomics Research Con (Nysgrc)
Date :  15 Mar 12  (Deposition) - 11 Apr 12  (Release) - 11 Apr 12  (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,D  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  B,C  (1x)
Biol. Unit 5:  C,D  (1x)
Keywords :  Nad(P)-Binding, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium (Nysgrc), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Kumar, N. Banu, R. Bhosle, J. Bonanno, S. Chamala, S. Chowdhury, A. Gizzi, S. Glen, J. Hammonds, B. Hillerich, J. D. Love, B. Matikainen R. Seidel, R. Toro, W. Zencheck, S. C. Almo
Crystal Structure Of A Probable Sorbitol Dehydrogenase From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE SORBITOL DEHYDROGENASE (L-IDITOL 2-DEHYDROGENASE)
    Chains: A, B, C, D
    EC Number: 1.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMOS, R02441, SMC01500
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 45)

Asymmetric Unit (3, 45)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 41)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 19)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (2, 20)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 4 (2, 22)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 5 (2, 21)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:47 , GLY A:51 , ALA A:54 , HOH A:444 , HOH A:457 , HOH A:468BINDING SITE FOR RESIDUE NA A 301
02AC2SOFTWAREGLN A:141 , ALA A:142 , ARG A:145 , GLU A:147BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWARELYS A:2 , ARG A:3 , ARG D:3BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREALA B:47 , GLY B:51 , ALA B:54 , HOH B:421 , HOH B:479 , HOH B:495BINDING SITE FOR RESIDUE NA B 301
05AC5SOFTWAREGLN B:141 , ALA B:142 , ARG B:145 , GLU B:147BINDING SITE FOR RESIDUE EDO B 302
06AC6SOFTWARETYR A:104 , PHE A:108 , ALA A:109 , TYR B:104 , PHE B:108 , HOH B:503 , HOH B:508BINDING SITE FOR RESIDUE EDO B 303
07AC7SOFTWARELYS B:7 , ASP B:82 , GLY B:133 , HOH B:445 , HOH B:496BINDING SITE FOR RESIDUE EDO B 304
08AC8SOFTWAREGLY A:143 , ARG A:144 , ARG A:145 , SER B:162 , GLN B:165 , EDO B:306 , HOH B:424 , HOH B:451 , HOH B:452BINDING SITE FOR RESIDUE EDO B 305
09AC9SOFTWAREGLN A:165 , GLY B:143 , ARG B:144 , ARG B:145 , EDO B:305 , HOH B:411 , HOH B:451 , HOH B:452BINDING SITE FOR RESIDUE EDO B 306
10BC1SOFTWAREVAL B:75 , GLN B:125BINDING SITE FOR RESIDUE EDO B 307
11BC2SOFTWAREALA C:47 , GLY C:51 , ALA C:54 , HOH C:492 , HOH C:497 , HOH C:512BINDING SITE FOR RESIDUE NA C 301
12BC3SOFTWARETYR C:104 , PHE C:108 , ALA C:109 , HOH C:469 , TYR D:104 , GLU D:105 , PHE D:108BINDING SITE FOR RESIDUE EDO C 302
13BC4SOFTWAREARG C:16 , ASP C:39 , GLU C:41 , ARG C:42BINDING SITE FOR RESIDUE EDO C 303
14BC5SOFTWARELYS C:7 , ASP C:82 , GLY C:133 , HOH C:485 , HOH C:490BINDING SITE FOR RESIDUE EDO C 304
15BC6SOFTWARESER C:8 , ALA C:78 , GLY C:80 , LEU C:81 , ASP C:82 , GLN C:129 , ARG C:131BINDING SITE FOR RESIDUE EDO C 305
16BC7SOFTWAREALA D:47 , GLY D:51 , ALA D:54 , EDO D:304 , HOH D:415BINDING SITE FOR RESIDUE NA D 301
17BC8SOFTWAREASP D:92 , LEU D:93 , ALA D:94 , ILE D:99 , LEU D:149 , VAL D:150 , ALA D:151 , ILE D:152 , TYR D:153 , HOH D:426BINDING SITE FOR RESIDUE EDO D 302
18BC9SOFTWAREPRO D:218 , GLY D:253 , ASN D:254 , TRP D:255 , HOH D:437BINDING SITE FOR RESIDUE EDO D 303
19CC1SOFTWAREGLY B:6 , ALA D:47 , PRO D:52 , ALA D:54 , NA D:301 , HOH D:444BINDING SITE FOR RESIDUE EDO D 304
20CC2SOFTWAREILE C:99 , ARG C:101 , GLN D:64 , GLN D:120 , ARG D:124BINDING SITE FOR RESIDUE EDO D 305
21CC3SOFTWARESER C:162 , GLN C:165 , HOH C:418 , GLY D:143 , ARG D:144 , ARG D:145 , HOH D:448BINDING SITE FOR RESIDUE EDO D 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E6P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly D:132 -Gly D:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E6P)

(-) Exons   (0, 0)

(no "Exon" information available for 4E6P)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4e6pa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6p A   2 KRLEGKSALITGSARGIGRAFAEAYVREGATVAIADIDIERARQAAAEIGPAAYAVQmDVTRQDSIDAAIAATVEHAGGLDILVNNAALFDLAPIVEITRESYEKLFAINVAGTLFTLQAAARQmIAQGRGGKIINmASQAGRRGEALVAIYCATKAAVISLTQSAGLDLIKHRINVNAIAPGVVDGEHWDGVDALFARYENRPRGEKKRLVGEAVPFGRmGTAEDLTGmAIFLASAESDYIVSQTYNVDGGNWmS 257
                                    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    | 
                                                                                    59-MSE                                                            126-MSE     138-MSE                                                                             222-MSE  231-MSE                  256-MSE


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4e6pb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6p B   2 KRLEGKSALITGSARGIGRAFAEAYVREGATVAIADIDIERARQAAAEIGPAAYAVQmDVTRQDSIDAAIAATVEHAGGLDILVNNAALFDLAPIVEITRESYEKLFAINVAGTLFTLQAAARQmIAQGRGGKIINmASQAGRRGEALVAIYCATKAAVISLTQSAGLDLIKHRINVNAIAPGVVDGEHWDGVDALFARYENRPRGEKKRLVGEAVPFGRmGTAEDLTGmAIFLASAESDYIVSQTYNVDGGNWmS 257
                                    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    | 
                                                                                    59-MSE                                                            126-MSE     138-MSE                                                                             222-MSE  231-MSE                  256-MSE


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4e6pc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6p C   2 KRLEGKSALITGSARGIGRAFAEAYVREGATVAIADIDIERARQAAAEIGPAAYAVQmDVTRQDSIDAAIAATVEHAGGLDILVNNAALFDLAPIVEITRESYEKLFAINVAGTLFTLQAAARQmIAQGRGGKIINmASQAGRRGEALVAIYCATKAAVISLTQSAGLDLIKHRINVNAIAPGVVDGEHWDGVDALFARYENRPRGEKKRLVGEAVPFGRmGTAEDLTGmAIFLASAESDYIVSQTYNVDGGNWmS 257
                                    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    | 
                                                                                    59-MSE                                                            126-MSE     138-MSE                                                                             222-MSE  231-MSE                  256-MSE


Chain D from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4e6pd_ D: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e6p D   2 KRLEGKSALITGSARGIGRAFAEAYVREGATVAIADIDIERARQAAAEIGPAAYAVQmDVTRQDSIDAAIAATVEHAGGLDILVNNAALFDLAPIVEITRESYEKLFAINVAGTLFTLQAAARQmIAQGRGGKIINmASQAGRRGEALVAIYCATKAAVISLTQSAGLDLIKHRINVNAIAPGVVDGEHWDGVDALFARYENRPRGEKKRLVGEAVPFGRmGTAEDLTGmAIFLASAESDYIVSQTYNVDGGNWmS 257
                                    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    | 
                                                                                    59-MSE                                                            126-MSE     138-MSE                                                                             222-MSE  231-MSE                  256-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E6P)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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