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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE CARBONYL REDUCTASE SNIFFER OF CAENORHABDITIS ELEGANS
 
Authors :  Southeast Collaboratory For Structural Genomics (Secsg)
Date :  26 Jan 05  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Tyrosine-Dependent Oxidoreductase (Sdr Family), Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, S. Lu, J. Symersky, E. Karpova, Y. Zhang, D. Luo, Q. Zhou, W. Huang, C. -H. Luan, R. Gray, A. Arabshahi, A. Mckinstry, S. Qiu, Z. Cao, J. An, S. Li, G. Lin, J. Tsao, D. Johnson, M. Luo, Q. Shang, Y. Chen, M. Stinnett, R. Bunzel, M. Carson, T. Bray, L. Delucas
Crystal Structure Of The Putative Carbonyl Reductase Sniffer Of Caenorhabditis Elegans
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE CARBONYL REDUCTASE SNIFFER
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SNIFFER
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Other Details: APO-ENZYME
    Synonym: SNIFFER LIKE FAMILY MEMBER (5L996)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YO6)

(-) Sites  (0, 0)

(no "Site" information available for 1YO6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YO6)

(-) Exons   (0, 0)

(no "Exon" information available for 1YO6)

(-) 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:237
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:250
                                    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
         P90780_CAEEL     1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6a1 A:1-250 Putative carbonyl reductase sniffer                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...-------------hhhhhhhhhhhhhhhhhhhh..eee..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 A   1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGW-------------VEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   |     -       220       230       240       250
                                                                                                                                                                                                                                     204           218                                


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:250
                                    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
         P90780_CAEEL     1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6b_ B: Carbonyl reductase sniffer                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhh......eeeeee.....hhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..---------------hhhhhhhhhhhhhhhhhhh..eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 B   1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPG---------------EQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |      -       220       230       240       250
                                                                                                                                                                                                                                    203             219                               


Chain C from PDB  Type:PROTEIN  Length:240
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:250
                                    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
         P90780_CAEEL     1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6c_ C: Carbonyl reductase sniffer                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhh....eeeeee.....hhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee......----------hhhhhhhhhhhhhhhhhhhh..eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 C   1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQT----------VEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  -       220       230       240       250
                                                                                                                                                                                                                                        207        218                                


Chain D from PDB  Type:PROTEIN  Length:236
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:250
                                    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
         P90780_CAEEL     1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6d_ D: Carbonyl reductase sniffer                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhh......eeeeee................eeeee....hhhhhhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...--------------.hhhhhhhhhhhhhhhhhh.eeee...ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 D   1 MSPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGW--------------EQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   |     -       220       230       240       250
                                                                                                                                                                                                                                     204            219                               


Chain E from PDB  Type:PROTEIN  Length:235
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
         P90780_CAEEL     2 SPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6e_ E: Carbonyl reductase sniffer                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..--------------hhhhhhhhhhhhhh.hhhhh..eee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 E   2 SPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPG--------------VEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 |       -      |221       231       241         
                                                                                                                                                                                                                                   203            218                                


Chain F from PDB  Type:PROTEIN  Length:230
 aligned with P90780_CAEEL | P90780 from UniProtKB/TrEMBL  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
         P90780_CAEEL     2 SPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKSIKDSRVHVLPLTVTCDKSLDTFVSKVGEIVGSDGLSLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKESGDQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWVQTNLGGKNAALTVEQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
               SCOP domains d1yo6f_ F: Carbonyl reductase sniffer                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --adh_short-1yo6F01 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (1)
           Pfam domains (2) --adh_short-1yo6F02 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (2)
           Pfam domains (3) --adh_short-1yo6F03 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (3)
           Pfam domains (4) --adh_short-1yo6F04 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (4)
           Pfam domains (5) --adh_short-1yo6F05 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (5)
           Pfam domains (6) --adh_short-1yo6F06 F:4-191                                                                                                                                                                   --------------             -------------------------------- Pfam domains (6)
         Sec.struct. author ...eeee....hhhhhhhhhhhhh.....eeeeee.hhhhhh....--...eeeee....hhhhhhhhhhhhhhhhh..--.eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--........eeeee.hhhhh............hhhhhhhhhhhhhhhhhhhhhh.....eeeee.....-------------hhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yo6 F   2 SPGSVVVTGANRGIGLGLVQQLVKDKNIRHIIATARDVEKATELKS--DSRVHVLPLTVTCDKSLDTFVSKVGEIVGSD--SLLINNAGVLLSYGTNTEPNRAVIAEQLDVNTTSVVLLTQKLLPLLKNAASKE--DQLSVSRAAVITISSGLGSITDNTSGSAQFPVLAYRMSKAAINMFGRTLAVDLKDDNVLVVNFCPGWV-------------EQSTAELISSFNKLDNSHNGRFFMRNLKPYEF 250
                                    11        21        31        41     |  51        61        71        |- |      91       101       111       121       131   |  |141       151       161       171       181       191       201   |     -       221       231       241         
                                                                        47 50                            80 83                                                 135  |                                                                205           219                               
                                                                                                                                                                  138
   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  (2, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YO6)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1YO6)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1YO6)

(-) Related Entries Specified in the PDB File

1sny CARBONYL REDUCTASE SNIFFER OF DROSOPHILA MELANOGASTER
1spx PUTATIVE GLUCOSE DEHYDROGENASE OF CAENORHABDITIS ELEGANS RELATED ID: C55A6.5 RELATED DB: TARGETDB