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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A THIOL-DISULFIDE ISOMERASE FROM CORYNEBACTERIUM GLUTAMICUM TO 2.2A
 
Authors :  A. J. Stein, J. Osipiuk, A. Weger, G. Cobb, A. Joachimiak, Midwest Cent Structural Genomics (Mcsg)
Date :  04 Feb 10  (Deposition) - 16 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thiol, Isomerase, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, J. Osipiuk, A. Weger, G. Cobb, A. Joachimiak
The Crystal Structure Of A Thiol-Disulfide Isomerase From Corynebacterium Glutamicum To 2. 2A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOL-DISULFIDE ISOMERASE AND THIOREDOXINS
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CG1043, CGL0914
    Organism Common: BREVIBACTERIUM FLAVUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC 13932

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3CL5Ligand/IonCHLORIDE ION
4MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:54 , HIS A:57 , ARG A:58 , LYS A:95BINDING SITE FOR RESIDUE CL A 161
2AC2SOFTWAREGLN B:54 , LYS B:95BINDING SITE FOR RESIDUE CL B 161
3AC3SOFTWAREGLN C:54 , HIS C:57 , LYS C:95BINDING SITE FOR RESIDUE CL C 161
4AC4SOFTWAREGLN D:54 , HIS D:57 , LYS D:95BINDING SITE FOR RESIDUE CL D 161
5AC5SOFTWAREPRO D:103 , ARG D:104 , GLN D:107 , ARG D:108 , ILE D:109 , PRO D:110BINDING SITE FOR RESIDUE CL D 162
6AC6SOFTWAREGLU B:11 , LEU B:12 , ASP B:13 , GLU D:11 , ASP D:13BINDING SITE FOR RESIDUE CA B 162
7AC7SOFTWAREGLU B:11 , LEU B:12 , ASN B:25BINDING SITE FOR RESIDUE ACT B 163

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:121 -Pro A:122
2Thr B:121 -Pro B:122
3Thr C:121 -Pro C:122
4Thr D:121 -Pro D:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LOR)

(-) 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:154
 aligned with Q8NRX7_CORGL | Q8NRX7 from UniProtKB/TrEMBL  Length:160

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
         Q8NRX7_CORGL     4 LDNAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQMLCPGCVNHGVPQAQKIHRMIDESQVQVIGLHSVFEHHDVMTPEALKVFIDEFGIKFPVAVDMPREGQRIPSTMKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee......hhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhh....eeee........hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lor A   4 LDNAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQmLCPGCVNHGVPQAQKIHRmIDESQVQVIGLHSVFEHHDVmTPEALKVFIDEFGIKFPVAVDmPREGQRIPSTmKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
                                    13        23        33      | 43        53     |  63        73      | 83        93       103       113       123       133       143       153    
                                                               40-MSE             59-MSE               80-MSE               102-MSE    113-MSE                                        


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q8NRX7_CORGL | Q8NRX7 from UniProtKB/TrEMBL  Length:160

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
         Q8NRX7_CORGL     4 LDNAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQMLCPGCVNHGVPQAQKIHRMIDESQVQVIGLHSVFEHHDVMTPEALKVFIDEFGIKFPVAVDMPREGQRIPSTMKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee......hhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhh.....eeee........hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lor B   4 LDNAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQmLCPGCVNHGVPQAQKIHRmIDESQVQVIGLHSVFEHHDVmTPEALKVFIDEFGIKFPVAVDmPREGQRIPSTmKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
                                    13        23        33      | 43        53     |  63        73      | 83        93       103       113       123       133       143       153    
                                                               40-MSE             59-MSE               80-MSE               102-MSE    113-MSE                                        


Chain C from PDB  Type:PROTEIN  Length:152
 aligned with Q8NRX7_CORGL | Q8NRX7 from UniProtKB/TrEMBL  Length:160

    Alignment length:152
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155  
         Q8NRX7_CORGL     6 NAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQMLCPGCVNHGVPQAQKIHRMIDESQVQVIGLHSVFEHHDVMTPEALKVFIDEFGIKFPVAVDMPREGQRIPSTMKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee......hhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhh....eeee........hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lor C   6 NAPLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQmLCPGCVNHGVPQAQKIHRmIDESQVQVIGLHSVFEHHDVmTPEALKVFIDEFGIKFPVAVDmPREGQRIPSTmKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
                                    15        25        35    |   45        55   |    65        75    |   85        95      |105       115       125       135       145       155  
                                                             40-MSE             59-MSE               80-MSE               102-MSE    113-MSE                                        


Chain D from PDB  Type:PROTEIN  Length:150
 aligned with Q8NRX7_CORGL | Q8NRX7 from UniProtKB/TrEMBL  Length:160

    Alignment length:150
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
         Q8NRX7_CORGL     8 PLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQMLCPGCVNHGVPQAQKIHRMIDESQVQVIGLHSVFEHHDVMTPEALKVFIDEFGIKFPVAVDMPREGQRIPSTMKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) AhpC-TSA-3lorD01 D:8-136                                                                                                         --------------------- Pfam domains (1)
           Pfam domains (2) AhpC-TSA-3lorD02 D:8-136                                                                                                         --------------------- Pfam domains (2)
           Pfam domains (3) AhpC-TSA-3lorD03 D:8-136                                                                                                         --------------------- Pfam domains (3)
           Pfam domains (4) AhpC-TSA-3lorD04 D:8-136                                                                                                         --------------------- Pfam domains (4)
         Sec.struct. author ......eeee......hhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhh....eeee........hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lor D   8 PLLELDVQEWVNHEGLSNEDLRGKVVVVEVFQmLCPGCVNHGVPQAQKIHRmIDESQVQVIGLHSVFEHHDVmTPEALKVFIDEFGIKFPVAVDmPREGQRIPSTmKKYRLEGTPSIILADRKGRIRQVQFGQVDDFVLGLLLGSLLSET 157
                                    17        27        37  |     47        57 |      67        77  |     87        97    |  107     | 117       127       137       147       157
                                                           40-MSE             59-MSE               80-MSE               102-MSE    113-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 3LOR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NRX7_CORGL | Q8NRX7)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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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