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(-) Description

Title :  STRUCTURE OF THE YPO2259 PUTATIVE OXIDOREDUCTASE FROM YERSINIA PESTIS
 
Authors :  S. M. Anderson, Z. Wawrzak, E. Gordon, K. Kwon, A. Edwards, A. Savchenko W. F. Anderson, Center For Structural Genomics Of Infectious D
Date :  28 Nov 09  (Deposition) - 22 Dec 09  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Oxidoreductase Family, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Anderson, Z. Wawrzak, E. Gordon, K. Kwon, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Structure Of The Ypo2259 Putative Oxidoreductase From Yersinia Pestis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Gene: MVIM4, Y2101, YPO2259, YP_2055
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: CO92
    Synonym: PUTATIVE UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:201 , ARG A:222BINDING SITE FOR RESIDUE CL A 350

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:48 -Ala A:49
2Lys A:95 -Pro A:96
3Trp A:163 -Arg A:164
4Gly A:171 -Gly A:172
5Leu A:265 -Pro A:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KUX)

(-) 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:349
 aligned with Q7CIK0_YERPE | Q7CIK0 from UniProtKB/TrEMBL  Length:349

    Alignment length:352
                               1                                                                                                                                                                                                                                                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
         Q7CIK0_YERPE     - ---MADKIKVGLLGYGYASKTFHAPLIMGTPGLELAGVSSSDASKVHADWPAIPVVSDPQMLFNDPSIDLIVIPTPNDTHFPLAQSALAAGKHVVVDKPFTVTLSQANALKEHADDAGLLLSVFHNRRWDSDFLTLKTLLAEGSLGNVVYFESHFDRYRPEIRQRWREQAGAGGGIWYDLGPHLLDQALQLFGLPETLNVDLGMLRPGSQSVDYFHAVLSYPGQRVVLHSTVLAAAETARYIVHGTQGSYIKFGVDPQEDRLKAGERLPQADWGYDMRDGIVTLSHDNVLTEKPLLTLPGNYPAYYAGIRDAIWGTAPNPVPATEAIKVMELIELGIASDQQKKALPIIAKN 349
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------GFO_IDH_MocA-3kuxA01 A:5-122                                                                                          -----------GFO_IDH_MocA_C-3kuxA02 A:134-241                                                                            ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhh......ee.hhhhhhhh....eeee.....hhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.............---..hhhhhhhhhhhhhhhhhhh...eeeeeee..........eeeeeeee..eeeeeeee.........eeeee..eeeee....hhhhhhhh...............eeeeee....eeeeee......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kux A  -2 SNAmADKIKVGLLGYGYASKTFHAPLImGTPGLELAGVSSSDASKVHADWPAIPVVSDPQmLFNDPSIDLIVIPTPNDTHFPLAQSALAAGKHVVVDKPFTVTLSQANALKEHADDAGLLLSVFHNRRWDSDFLTLKTLLAEGSLGNVVYFESHFDRYRPEIRQRWREQ---GGGIWYDLGPHLLDQALQLFGLPETLNVDLGmLRPGSQSVDYFHAVLSYPGQRVVLHSTVLAAAETARYIVHGTQGSYIKFGVDPQEDRLKAGERLPQADWGYDmRDGIVTLSHDNVLTEKPLLTLPGNYPAYYAGIRDAIWGTAPNPVPATEAIKVmELIELGIASDQQKKALPIIAKN 349
                               |     7        17       |27        37        47        57|       67        77        87        97       107       117       127       137       147       157        |-  |    177       187       197   |   207       217       227       237       247       257       267      |277       287       297       307       317       327       337       347  
                               |                      25-MSE                           58-MSE                                                                                                     166 170                            201-MSE                                                                  274-MSE                                              327-MSE                  
                               1-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 3KUX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: ox_reductase_C (19)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7CIK0_YERPE | Q7CIK0)
molecular function
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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