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(-) Description

Title :  OXIDOREDUCTASE NMDSBA3 FROM NEISSERIA MENINGITIDIS
 
Authors :  J. P. Vivian, J. Scoullar, A. L. Robertson, S. P. Bottomley, J. Horne, Y. Chin, T. Velkov, J. Wielens, P. E. Thompson, S. Piek, E. Byres, T. Beddoe, M. C. J. Wilce, C. Kahler, J. Rossjohn, M. J. Scanlon
Date :  30 Apr 08  (Deposition) - 19 Aug 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Thioredoxin Fold, Dsba-Like, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Vivian, J. Scoullar, A. L. Robertson, S. P. Bottomley, J. Horne, Y. Chin, J. Wielens, P. E. Thompson, T. Velkov, S. Piek, E. Byres, T. Beddoe, M. C. Wilce, C. M. Kahler, J. Rossjohn, M. J. Scanlon
Structural And Biochemical Characterization Of The Oxidoreductase Nmdsba3 From Neisseria Meningitidis
J. Biol. Chem. V. 283 32452 2008
PubMed-ID: 18715864  |  Reference-DOI: 10.1074/JBC.M803990200
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DSBA3, UNP RESIDUES 20-214
    Gene: DSBA-3, NMB0407
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP B
    Organism Taxid: 491
    Strain: SEROGROUP B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ZNM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZNM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:151 -Pro A:152
2Thr B:151 -Pro B:152
3Thr C:151 -Pro C:152
4Thr D:151 -Pro D:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZNM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZNM)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZNM)

(-) 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:185
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:185
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
         Q9K0Z4_NEIMB    22 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERK 206
               SCOP domains d2znma_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee............eeeeeee..........hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znm A   3 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERK 187
                                    12        22        32        42        52        62     |  72 |      82        92       102       112       122 |     132      |142       152       162       172       182     
                                                                                            68-MSE |                                               124-MSE        139-MSE                                            
                                                                                                  74-MSE                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:185
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
         Q9K0Z4_NEIMB    22 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERK 206
               SCOP domains d2znmb_ B: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee............eeeeeee..........hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znm B   3 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERK 187
                                    12        22        32        42        52        62     |  72 |      82        92       102       112       122 |     132      |142       152       162       172       182     
                                                                                            68-MSE |                                               124-MSE        139-MSE                                            
                                                                                                  74-MSE                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:186
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:186
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
         Q9K0Z4_NEIMB    22 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERKR 207
               SCOP domains d2znmc_ C: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee............eeeeeee..........hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eee...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2znm C   3 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERKR 188
                                    12        22        32        42        52        62     |  72 |      82        92       102       112       122 |     132      |142       152       162       172       182      
                                                                                            68-MSE |                                               124-MSE        139-MSE                                             
                                                                                                  74-MSE                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:184
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
         Q9K0Z4_NEIMB    22 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREER 205
               SCOP domains d2znmd_ D: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------Thioredoxin_4-2znmD01 D:19-180                                                                                                                                    ------ Pfam domains (1)
           Pfam domains (2) ----------------Thioredoxin_4-2znmD02 D:19-180                                                                                                                                    ------ Pfam domains (2)
           Pfam domains (3) ----------------Thioredoxin_4-2znmD03 D:19-180                                                                                                                                    ------ Pfam domains (3)
           Pfam domains (4) ----------------Thioredoxin_4-2znmD04 D:19-180                                                                                                                                    ------ Pfam domains (4)
         Sec.struct. author ......eee............eeeeeee..........hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znm D   3 LTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREER 186
                                    12        22        32        42        52        62     |  72 |      82        92       102       112       122 |     132      |142       152       162       172       182    
                                                                                            68-MSE |                                               124-MSE        139-MSE                                           
                                                                                                  74-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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZNM)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9K0Z4_NEIMB | Q9K0Z4)
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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(-) Related Entries Specified in the PDB File

1dsb DSBA PROTEIN FROM E.COLI