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(-) Description

Title :  CRYSTAL STRUCTURE OF THIOREDOXIN FROM METHANOSARCINA MAZEI
 
Authors :  B. Syed Ibrahim, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Jun 09  (Deposition) - 30 Jun 09  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nysgxrc, Psi-Ii, Reduced Form, Thioredoxin, 11215H, Protein Structure Initiative, Crystal Structure, Structural Genomics, New York Sgx Research Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Syed Ibrahim, S. K. Burley, S. Swaminathan
Crystal Structure Of Thioredoxin From Methanosarcina Mazei
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: TOP10
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MM_2079
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:66 , TRP B:67 , GLU B:70BINDING SITE FOR RESIDUE EDO B 142
2AC2SOFTWAREPRO A:88 , HOH A:193 , GLY B:73 , VAL B:74 , GLN B:75 , GLY B:76 , THR B:79 , GLU B:91 , VAL B:93 , HOH B:184 , HOH B:187BINDING SITE FOR RESIDUE EDO B 143
3AC3SOFTWARETRP A:90 , MSE A:108 , TRP B:90 , GLN B:92BINDING SITE FOR RESIDUE EDO B 144

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HZ4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:3 -Ser A:4
2Thr A:77 -Pro A:78
3Thr B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 3HZ4)

(-) 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:120
 aligned with Q8PV92_METMA | Q8PV92 from UniProtKB/TrEMBL  Length:130

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q8PV92_METMA     2 NGSSIIEFEDMTWSQQVEDSKKPVVVMFYSPACPYCKAMEPYFEEYAKEYGSSAVFGRINIATNPWTAEKYGVQGTPTFKFFCHGRPVWEQVGQIYPSILKNAVRDMLQHGEECIRKSTP 121
               SCOP domains d3hz4a_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh..ee.eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hz4 A   2 NGSSIIEFEDmTWSQQVEDSKKPVVVmFYSPACPYCKAmEPYFEEYAKEYGSSAVFGRINIATNPWTAEKYGVQGTPTFKFFCHGRPVWEQVGQIYPSILKNAVRDmLQHGEECIRKSTP 121
                                    11|       21      | 31        41        51        61        71        81        91       101      |111       121
                                     12-MSE          28-MSE      40-MSE                                                             108-MSE         


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q8PV92_METMA | Q8PV92 from UniProtKB/TrEMBL  Length:130

    Alignment length:120
                                    14        24        34        44        54        64        74        84        94       104       114       124
         Q8PV92_METMA     5 SIIEFEDMTWSQQVEDSKKPVVVMFYSPACPYCKAMEPYFEEYAKEYGSSAVFGRINIATNPWTAEKYGVQGTPTFKFFCHGRPVWEQVGQIYPSILKNAVRDMLQHGEECIRKSTPVGQ 124
               SCOP domains d3hz4b_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....hhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hz4 B   5 SIIEFEDmTWSQQVEDSKKPVVVmFYSPACPYCKAmEPYFEEYAKEYGSSAVFGRINIATNPWTAEKYGVQGTPTFKFFCHGRPVWEQVGQIYPSILKNAVRDmLQHGEECIRKSTPVGQ 124
                                   |14        24   |    34     |  44        54        64        74        84        94       104   |   114       124
                                  12-MSE          28-MSE      40-MSE                                                             108-MSE
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  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  (0, 0)

(no "CATH Domain" information available for 3HZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HZ4)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8PV92_METMA | Q8PV92)
molecular function
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    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.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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