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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT CHAIN DEHYDROGENASE (YCIK) FROM SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 IN COMPLEX WITH NADP AND ACETATE.
 
Authors :  G. Minasov, A. Halavaty, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  14 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Short Chain Dehydrogenase, Nadp, Acetate, Idp00971, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, A. Halavaty, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Short Chain Dehydrogenase (Ycik) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str Lt2 In Complex With Nadp And Acetate.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT CHAIN DEHYDROGENASE YCIK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: STM1717, YCIK
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: PUTATIVE OXOACYL-(ACYL CARRIER PROTEIN) REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3EOH2Ligand/IonETHANOL
4MSE19Mod. Amino AcidSELENOMETHIONINE
5NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , SER A:21 , ASP A:22 , GLY A:23 , ILE A:24 , ARG A:44 , LYS A:48 , LEU A:69 , ASP A:70 , LEU A:71 , LEU A:72 , ASN A:99 , ALA A:100 , GLY A:101 , THR A:150 , SER A:151 , TYR A:165 , LYS A:169 , PRO A:195 , GLY A:196 , GLY A:197 , THR A:198 , THR A:200 , MSE A:202 , ARG A:203 , ACT A:255 , HOH A:278 , HOH A:287 , HOH A:311 , HOH A:324 , HOH A:402 , HOH A:422 , HOH A:445 , HOH A:459BINDING SITE FOR RESIDUE NAP A 254
2AC2SOFTWARESER A:152 , TYR A:165 , ARG A:203 , NAP A:254 , EOH A:257BINDING SITE FOR RESIDUE ACT A 255
3AC3SOFTWAREARG A:159 , TRP A:162 , HOH A:269 , HOH A:286 , ASN B:185 , HOH B:433BINDING SITE FOR RESIDUE ACT A 256
4AC4SOFTWARESER A:153 , ARG A:159 , ARG A:203 , ARG A:247 , GLY A:250 , ACT A:255 , HOH A:403BINDING SITE FOR RESIDUE EOH A 257
5AC5SOFTWARETHR A:209 , ARG B:235BINDING SITE FOR RESIDUE EOH A 258
6AC6SOFTWAREARG A:85 , HIS A:89 , GLN B:7BINDING SITE FOR RESIDUE CL A 259
7AC7SOFTWAREGLY B:19 , SER B:21 , ASP B:22 , GLY B:23 , ILE B:24 , ARG B:44 , LYS B:48 , LEU B:69 , ASP B:70 , LEU B:71 , LEU B:72 , ASN B:99 , ALA B:100 , GLY B:101 , VAL B:123 , THR B:150 , SER B:151 , TYR B:165 , LYS B:169 , PRO B:195 , GLY B:196 , GLY B:197 , THR B:198 , THR B:200 , MSE B:202 , ARG B:203 , ACT B:255 , HOH B:278 , HOH B:319 , HOH B:325 , HOH B:329 , HOH B:341 , HOH B:408 , HOH B:451 , HOH B:455 , HOH B:480BINDING SITE FOR RESIDUE NAP B 254
8AC8SOFTWARESER B:152 , TYR B:165 , ARG B:203 , NAP B:254 , HOH B:271 , HOH B:294BINDING SITE FOR RESIDUE ACT B 255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IAH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IAH)

(-) 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:253
 aligned with Q7CQG2_SALTY | Q7CQG2 from UniProtKB/TrEMBL  Length:253

    Alignment length:253
                                    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   
         Q7CQG2_SALTY     1 MHYQPKQDLLQNRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRRVAQHIADEQHVQPQWFTLDLLTCTAEECRQVADRIAAHYPRLDGVLHNAGLLGEIGPMSEQDPQIWQDVMQVNVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYATSKFATEGMMQVLADEYQNRSLRVNCINPGGTRTSMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGIAQ 253
               SCOP domains d3iaha_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains -3iahA00 A:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iah A   1 mHYQPKQDLLQNRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRRVAQHIADEQHVQPQWFTLDLLTCTAEECRQVADRIAAHYPRLDGVLHNAGLLGEIGPmSEQDPQIWQDVmQVNVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYATSKFATEGmmQVLADEYQNRSLRVNCINPGGTRTSmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGIAQ 253
                            |       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   
                            |                                                                                                         109-MSE     121-MSE  130-MSE                                      175-MSE                    202-MSE             222-MSE  |       239-MSE          
                            1-MSE                                                                                                                                                                        176-MSE                                              229-MSE                    


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q7CQG2_SALTY | Q7CQG2 from UniProtKB/TrEMBL  Length:253

    Alignment length:252
                                    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  
         Q7CQG2_SALTY     2 HYQPKQDLLQNRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRRVAQHIADEQHVQPQWFTLDLLTCTAEECRQVADRIAAHYPRLDGVLHNAGLLGEIGPMSEQDPQIWQDVMQVNVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYATSKFATEGMMQVLADEYQNRSLRVNCINPGGTRTSMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGIAQ 253
               SCOP domains d3iahb_ B: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3iahB00 B:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3iah B   2 HYQPKQDLLQNRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRRVAQHIADEQHVQPQWFTLDLLTCTAEECRQVADRIAAHYPRLDGVLHNAGLLGEIGPmSEQDPQIWQDVmQVNVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYATSKFATEGmmQVLADEYQNRSLRVNCINPGGTRTSmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGIAQ 253
                                    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  
                                                                                                                                     109-MSE     121-MSE  130-MSE                                      175-MSE                    202-MSE             222-MSE  |       239-MSE          
                                                                                                                                                                                                        176-MSE                                              229-MSE
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CQG2_SALTY | Q7CQG2)
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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(-) Related Entries Specified in the PDB File

3g1t CRYSTAL STRUCTURE OF SHORT CHAIN DEHYDROGENASE FROM SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI STR. CT18. RELATED ID: IDP00971 RELATED DB: TARGETDB