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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE/REDUCTASE OF UNKNOWN FUNCTION FROM CAENORHABDITIS ELEGANS WITH COFACTOR
 
Authors :  N. Schormann, J. Zhou, E. Karpova, Y. Zhang, J. Symersky, B. Bunzel, W. - Y. Huang, A. Arabshahi, S. Qiu, C. -H. Luan, R. Gray, M. Carson, J. Tsao, M. Luo, D. Johnson, S. Lu, G. Lin, D. Luo, Z. Cao, S. Li, A. Mckinstry, Q. Shang, Y. -J. Chen, T. Bray, L. Nagy, L. Delucas, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  29 Sep 04  (Deposition) - 12 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Parrallel Beta-Sheet Of Seven Strands In The Order 3214567; Three Alpha-Helices On Either Side Of Beta-Sheet; Seventh Alpha-Helix On Top Of Beta-Sheet, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, J. Zhou, E. Karpova, Y. Zhang, J. Symersky, B. Bunzel, W. -Y. Huang, A. Arabshahi, S. Qiu, C. -H. Luan, R. Gray, M. Carson, J. Tsao, M. Luo, D. Johnson, S. Lu, G. Lin, D. Luo, Z. Cao, S. Li, A. Mckinstry, Q. Shang, Y. -J. Chen, T. Bray, L. Nagy, L. Delucas
Crystal Structure Of Short-Chain Dehydrogenase/Reductase Of Unknown Function From Caenorhabditis Elegans With Cofactor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHORT-CHAIN REDUCTASE FAMILY MEMBER (5D234)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: R05D8.7
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Other Details: SEE REMARK 400
    Synonym: HYPOTHETICAL PROTEIN R05D8.7

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , SER A:14 , SER A:15 , ASN A:16 , GLY A:17 , ILE A:18 , GLY A:37 , ARG A:38 , SER A:39 , ARG A:42 , ALA A:65 , ASP A:66 , VAL A:67 , THR A:68 , ASN A:93 , ALA A:94 , GLY A:95 , LEU A:120 , VAL A:146 , SER A:147 , SER A:148 , TYR A:162 , LYS A:166 , PRO A:192 , GLY A:193 , MET A:194 , VAL A:195 , THR A:197 , GLY A:198 , PHE A:199 , HOH A:1284 , HOH A:1285 , HOH A:1306 , HOH A:1315 , HOH A:1335 , HOH A:1348 , HOH A:1377BINDING SITE FOR RESIDUE NDP A 1281
2AC2SOFTWAREGLY B:13 , SER B:14 , SER B:15 , ASN B:16 , GLY B:17 , ILE B:18 , GLY B:37 , ARG B:38 , SER B:39 , ARG B:42 , ALA B:65 , ASP B:66 , VAL B:67 , ASN B:93 , ALA B:94 , GLY B:95 , LEU B:120 , SER B:147 , SER B:148 , TYR B:162 , LYS B:166 , PRO B:192 , GLY B:193 , MET B:194 , VAL B:195 , THR B:197 , GLY B:198 , PHE B:199 , HOH B:2298 , HOH B:2311 , HOH B:2352 , HOH B:2367 , HOH B:2405BINDING SITE FOR RESIDUE NDP B 2281
3AC3SOFTWAREGLY C:13 , SER C:14 , SER C:15 , ASN C:16 , GLY C:17 , ILE C:18 , GLY C:37 , ARG C:38 , SER C:39 , ARG C:42 , ALA C:65 , ASP C:66 , VAL C:67 , ASN C:93 , ALA C:94 , GLY C:95 , LEU C:120 , SER C:147 , SER C:148 , TYR C:162 , LYS C:166 , PRO C:192 , GLY C:193 , MET C:194 , VAL C:195 , THR C:197 , GLY C:198 , PHE C:199 , HOH C:3302 , HOH C:3313 , HOH C:3317 , HOH C:3319 , HOH C:3349 , HOH C:3357BINDING SITE FOR RESIDUE NDP C 3281
4AC4SOFTWAREGLY D:13 , SER D:14 , SER D:15 , ASN D:16 , GLY D:17 , ILE D:18 , GLY D:37 , ARG D:38 , SER D:39 , ARG D:42 , ALA D:65 , ASP D:66 , VAL D:67 , THR D:68 , ASN D:93 , ALA D:94 , GLY D:95 , LEU D:120 , SER D:147 , SER D:148 , TYR D:162 , LYS D:166 , PRO D:192 , GLY D:193 , MET D:194 , VAL D:195 , THR D:197 , GLY D:198 , PHE D:199 , HOH D:4286 , HOH D:4287 , HOH D:4304 , HOH D:4310 , HOH D:4327 , HOH D:4335 , HOH D:4382BINDING SITE FOR RESIDUE NDP D 4281

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XKQ)

(-) 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:272
 aligned with Q9N5G4_CAEEL | Q9N5G4 from UniProtKB/TrEMBL  Length:280

    Alignment length:272
                                    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       261       271  
         Q9N5G4_CAEEL     2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHDV 273
               SCOP domains d1xkqa_ A: Hypothetical protein R05D8.7                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1xkqA00 A:2-273 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkq A   2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHDV 273
                                    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       261       271  


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q9N5G4_CAEEL | Q9N5G4 from UniProtKB/TrEMBL  Length:280

    Alignment length:271
                                    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       261       271 
         Q9N5G4_CAEEL     2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
               SCOP domains d1xkqb_ B: Hypothetical protein R05D8.7                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xkqB00 B:2-272 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkq B   2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
                                    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       261       271 


Chain C from PDB  Type:PROTEIN  Length:271
 aligned with Q9N5G4_CAEEL | Q9N5G4 from UniProtKB/TrEMBL  Length:280

    Alignment length:271
                                    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       261       271 
         Q9N5G4_CAEEL     2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
               SCOP domains d1xkqc_ C: Hypothetical protein R05D8.7                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xkqC00 C:2-272 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkq C   2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
                                    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       261       271 


Chain D from PDB  Type:PROTEIN  Length:271
 aligned with Q9N5G4_CAEEL | Q9N5G4 from UniProtKB/TrEMBL  Length:280

    Alignment length:271
                                    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       261       271 
         Q9N5G4_CAEEL     2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
               SCOP domains d1xkqd_ D: Hypothetical protein R05D8.7                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xkqD00 D:2-272 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----------adh_short_C2-1xkqD01 D:12-263                                                                                                                                                                                                                               --------- Pfam domains (1)
           Pfam domains (2) ----------adh_short_C2-1xkqD02 D:12-263                                                                                                                                                                                                                               --------- Pfam domains (2)
           Pfam domains (3) ----------adh_short_C2-1xkqD03 D:12-263                                                                                                                                                                                                                               --------- Pfam domains (3)
           Pfam domains (4) ----------adh_short_C2-1xkqD04 D:12-263                                                                                                                                                                                                                               --------- Pfam domains (4)
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkq D   2 PRFSNKTVIITGSSNGIGRTTAILFAQEGANVTITGRSSERLEETRQIILKSGVSEKQVNSVVADVTTEDGQDQIINSTLKQFGKIDVLVNNAGAAIPDAFGTTGTDQGIDIYHKTLKLNLQAVIEMTKKVKPHLVASKGEIVNVSSIVAGPQAQPDFLYYAIAKAALDQYTRSTAIDLAKFGIRVNSVSPGMVETGFTNAMGMPDQASQKFYNFMASHKECIPIGAAGKPEHIANIILFLADRNLSFYILGQSIVADGGTSLVMGTQAHD 272
                                    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       261       271
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9N5G4_CAEEL | Q9N5G4)
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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  1xkq
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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 1XKQ)

(-) Related Entries Specified in the PDB File

1ooe A C. ELEGANS PROTEIN (DIHYDROPTERIDINE REDUCTASE) FROM THE SAME FAMILY (SDR FAMILY) RELATED ID: R05D8.7 RELATED DB: TARGETDB
1spx A C. ELEGANS PROTEIN (PUTATIVE GLUCOSE DEHYDROGENASE) FROM THE SAME FAMILY (SDR FAMILY)
1xhl A C. ELEGANS PROTEIN (PUTATIVE TROPINONE REDUCTASE II) FROM THE SAME FAMILY (SDR FAMILY)