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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YHDH OXIDOREDUCTASE FROM SALMONELLA ENTERICA IN COMPLEX WITH NADP
 
Authors :  S. M. Anderson, Z. Wawrzak, S. Peterson, O. Onopriyenko, T. Skarina, W. F. Anderson, A. Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  12 Jul 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Psi, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Anderson, Z. Wawrzak, S. Peterson, O. Onopriyenko, T. Skarina, W. F. Anderson, A. Savchenko
Crystal Structure Of The Yhdh Oxidoreductase From Salmonell Enterica In Complex With Nadp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-CODONPLUS(DE3)-RIL
    Expression System Taxid469008
    GeneYHDH, STM3376
    Organism ScientificSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid99287
    StrainLT2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:41 , THR A:126 , THR A:130 , GLY A:154 , SER A:156 , GLY A:157 , GLY A:158 , VAL A:159 , SER A:178 , GLY A:179 , ARG A:180 , ARG A:198 , THR A:218 , VAL A:219 , CYS A:240 , GLY A:241 , LEU A:242 , ALA A:243 , GLY A:244 , VAL A:265 , ASP A:266 , SER A:267 , ASN A:313 , HOH A:326 , HOH A:336 , HOH A:392 , HOH A:418 , HOH A:458 , HOH A:462 , HOH A:491 , HOH A:503 , ILE B:256BINDING SITE FOR RESIDUE NAP A 330
2AC2SOFTWAREILE A:256 , TYR B:41 , THR B:126 , THR B:130 , GLY B:154 , SER B:156 , GLY B:157 , GLY B:158 , VAL B:159 , SER B:178 , GLY B:179 , ARG B:180 , ARG B:198 , THR B:218 , CYS B:240 , GLY B:241 , LEU B:242 , ALA B:243 , VAL B:265 , SER B:267 , ILE B:310 , ASN B:313 , HOH B:333 , HOH B:341 , HOH B:343 , HOH B:461 , HOH B:465 , HOH B:468 , HOH B:474BINDING SITE FOR RESIDUE NAP B 330

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NX4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:57 -Pro A:58
2Phe B:57 -Pro B:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NX4)

(-) Exons   (0, 0)

(no "Exon" information available for 3NX4)

(-) 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:324
 aligned with Q7CPM2_SALTY | Q7CPM2 from UniProtKB/TrEMBL  Length:324

    Alignment length:324
                                    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       260       270       280       290       300       310       320    
         Q7CPM2_SALTY     1 MQALILEQQDGKTLASVQHLEESQLPAGDVTVDVHWSSLNYKDALAITGKGKIIRHFPMIPGIDFAGTVHASEDPRFHAGQEVLLTGWGVGENHWGGLAERARVKGDWLVALPAGLSSRNAMIIGTAGFTAMLCVMALEDAGIRPQDGEVVVTGASGGVGSTAVALLHKLGYQVAAVSGRESTHGYLKSLGANRILSRDEFAESRPLEKQLWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFALPTTVMPFILRNVRLQGVDSVMTPPARRAEAWARLVKDLPESFYAQAATEITLADAPKFADAIINNQVQGRTLVKIK 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee.hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nx4 A   1 mQALILEQQDGKTLASVQHLEESQLPAGDVTVDVHWSSLNYKDALAITGKGKIIRHFPmIPGIDFAGTVHASEDPRFHAGQEVLLTGWGVGENHWGGLAERARVKGDWLVALPAGLSSRNAmIIGTAGFTAmLCVmALEDAGIRPQDGEVVVTGASGGVGSTAVALLHKLGYQVAAVSGRESTHGYLKSLGANRILSRDEFAESRPLEKQLWAGAIDTVGDKVLAKVLAQmNYGGCVAACGLAGGFALPTTVmPFILRNVRLQGVDSVmTPPARRAEAWARLVKDLPESFYAQAATEITLADAPKFADAIINNQVQGRTLVKIK 324
                            |       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  |    260       270       280       290       300       310       320    
                            |                                                        59-MSE                                                        122-MSE   132-MSE                                                                                            231-MSE               253-MSE         269-MSE                                                   
                            1-MSE                                                                                                                                136-MSE                                                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q7CPM2_SALTY | Q7CPM2 from UniProtKB/TrEMBL  Length:324

    Alignment length:324
                                    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       260       270       280       290       300       310       320    
         Q7CPM2_SALTY     1 MQALILEQQDGKTLASVQHLEESQLPAGDVTVDVHWSSLNYKDALAITGKGKIIRHFPMIPGIDFAGTVHASEDPRFHAGQEVLLTGWGVGENHWGGLAERARVKGDWLVALPAGLSSRNAMIIGTAGFTAMLCVMALEDAGIRPQDGEVVVTGASGGVGSTAVALLHKLGYQVAAVSGRESTHGYLKSLGANRILSRDEFAESRPLEKQLWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFALPTTVMPFILRNVRLQGVDSVMTPPARRAEAWARLVKDLPESFYAQAATEITLADAPKFADAIINNQVQGRTLVKIK 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------ADH_N-3nx4B01 B:27-94                                               ---------------------------------------------------------------ADH_zinc_N-3nx4B03 B:158-284                                                                                                   ---------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------ADH_N-3nx4B02 B:27-94                                               ---------------------------------------------------------------ADH_zinc_N-3nx4B04 B:158-284                                                                                                   ---------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee..eeeeeeee.hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nx4 B   1 mQALILEQQDGKTLASVQHLEESQLPAGDVTVDVHWSSLNYKDALAITGKGKIIRHFPmIPGIDFAGTVHASEDPRFHAGQEVLLTGWGVGENHWGGLAERARVKGDWLVALPAGLSSRNAmIIGTAGFTAmLCVmALEDAGIRPQDGEVVVTGASGGVGSTAVALLHKLGYQVAAVSGRESTHGYLKSLGANRILSRDEFAESRPLEKQLWAGAIDTVGDKVLAKVLAQmNYGGCVAACGLAGGFALPTTVmPFILRNVRLQGVDSVmTPPARRAEAWARLVKDLPESFYAQAATEITLADAPKFADAIINNQVQGRTLVKIK 324
                            |       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  |    260       270       280       290       300       310       320    
                            1-MSE                                                    59-MSE                                                        122-MSE   132-MSE                                                                                            231-MSE               253-MSE         269-MSE                                                   
                                                                                                                                                                 136-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  (0, 0)

(no "SCOP Domain" information available for 3NX4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NX4)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GroES (70)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CPM2_SALTY | Q7CPM2)
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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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