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(-) Description

Title :  IDENTIFICATION OF A DISULFIDE SWITCH IN BSSCO, A MEMBER OF THE SCO FAMILY OF CYTOCHROME C OXIDASE ASSEMBLY PROTEINS
 
Authors :  Q. Ye, I. Imriskova-Sosova, B. C. Hill, Z. Jia, Montreal-Kingston Bac Structural Genomics Initiative (Bsgi)
Date :  12 Nov 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Thioredoxin-Like Fold, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Ye, I. Imriskova-Sosova, B. C. Hill, Z. Jia
Identification Of A Disulfide Switch In Bssco, A Member Of The Sco Family Of Cytochrome C Oxidase Assembly Proteins
Biochemistry V. 44 2934 2005
PubMed-ID: 15723536  |  Reference-DOI: 10.1021/BI0480537

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YPMQ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNM137
    Expression System Taxid: 562
    Expression System Vector: PGEX-4T3
    Expression System Vector Type: PLASMID
    Gene: YPMQ
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: DH5F
    Synonym: BSSCO

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB
Biological Unit 4 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1CA14Ligand/IonCALCIUM ION
2CD5Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:161 , HIS B:55 , CA B:1011 , HOH B:1036 , HOH B:1203BINDING SITE FOR RESIDUE CD B 1000
02AC2SOFTWAREHIS A:55 , CA A:1015 , HOH A:1035 , HOH A:1186 , ASP B:161BINDING SITE FOR RESIDUE CD A 1001
03AC3SOFTWAREGLU A:14 , GLU B:114 , HOH B:1208 , HOH B:1215BINDING SITE FOR RESIDUE CD A 1002
04AC4SOFTWAREGLU A:113 , LYS A:125 , HOH A:1029BINDING SITE FOR RESIDUE CD A 1003
05AC5SOFTWARELYS A:6 , ASP A:162 , ASP A:166 , HOH A:1183BINDING SITE FOR RESIDUE CD A 1004
06AC6SOFTWARETHR A:17 , CA A:1010 , HOH A:1044 , HOH A:1073 , HOH A:1162 , THR B:17 , HOH B:1020 , HOH B:1039BINDING SITE FOR RESIDUE CA A 1005
07AC7SOFTWAREHOH A:1033 , HOH A:1138 , GLU B:29 , HOH B:1153 , HOH B:1214BINDING SITE FOR RESIDUE CA B 1006
08AC8SOFTWAREASP B:58 , HOH B:1089 , HOH B:1107 , HOH B:1122 , HOH B:1138BINDING SITE FOR RESIDUE CA B 1007
09AC9SOFTWAREGLU A:29 , HOH A:1187 , HOH B:1025BINDING SITE FOR RESIDUE CA A 1008
10BC1SOFTWAREASP A:58 , HOH A:1058 , HOH A:1079 , HOH B:1219BINDING SITE FOR RESIDUE CA A 1009
11BC2SOFTWARETHR A:17 , GLY A:106 , CA A:1005 , HOH A:1073 , HOH A:1162 , THR B:17BINDING SITE FOR RESIDUE CA A 1010
12BC3SOFTWARELYS A:62 , ASP A:161 , HOH A:1080 , HIS B:55 , TYR B:160 , CD B:1000BINDING SITE FOR RESIDUE CA B 1011
13BC4SOFTWARESER A:108 , PHE B:16 , LEU B:28 , GLU B:29 , HOH B:1102BINDING SITE FOR RESIDUE CA B 1012
14BC5SOFTWAREASP A:69 , HOH A:1124 , HOH A:1184BINDING SITE FOR RESIDUE CA A 1013
15BC6SOFTWAREASP A:78 , HOH A:1048 , HOH A:1109BINDING SITE FOR RESIDUE CA A 1014
16BC7SOFTWAREHIS A:55 , TYR A:160 , CD A:1001 , HOH A:1064 , LYS B:62 , ASP B:161BINDING SITE FOR RESIDUE CA A 1015
17BC8SOFTWAREPRO A:15 , PHE A:16 , GLU A:29 , HOH A:1123 , SER B:108 , HOH B:1022BINDING SITE FOR RESIDUE CA A 1016
18BC9SOFTWAREASP B:151 , HOH B:1181BINDING SITE FOR RESIDUE CA B 1017
19CC1SOFTWAREASP B:162 , ASP B:166 , HOH B:1100BINDING SITE FOR RESIDUE CA B 1018

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XZO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XZO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XZO)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.SCO1_BACSU26-191
 		  2A:7-172
B:7-172
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.SCO1_BACSU26-191
 		  1A:7-172
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.SCO1_BACSU26-191
 		  1-
B:7-172
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.SCO1_BACSU26-191
 		  4A:7-172
B:7-172
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.SCO1_BACSU26-191
 		  2A:7-172
B:7-172

(-) Exons   (0, 0)

(no "Exon" information available for 1XZO)

(-) 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:172
 aligned with SCO1_BACSU | P54178 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:172
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SCO1_BACSU    22 QQIKDPLNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTNCETICPPMTAHMTDLQKKLKAENIDVRIISFSVDPENDKPKQLKKFAANYPLSFDNWDFLTGYSQSEIEEFALKSFKAIVKKPEGEDQVIHQSSFYLVGPDGKVLKDYNGVENTPYDDIISDVKSASTLK 193
               SCOP domains d1xzoa1 A:3-174 Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....eee.....eee.hhhh...eeeeee...........hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh....hhh.eeee...hhhhhhhhhhhhhh................eeeee....eeeeeee.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----THIOREDOXIN_2  PDB: A:7-172 UniProt: 26-191                                                                                                                           -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xzo A   3 QQIKDPLNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTNCETICPPMTAHMTDLQKKLKAENIDVRIISFSVDPENDKPKQLKKFAANYPLSFDNWDFLTGYSQSEIEEFALKSFKAIVKKPEGEDQVIHQSSFYLVGPDGKVLKDYNGVENTPYDDIISDVKSASTLK 174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with SCO1_BACSU | P54178 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:172
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SCO1_BACSU    22 QQIKDPLNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTNCETICPPMTAHMTDLQKKLKAENIDVRIISFSVDPENDKPKQLKKFAANYPLSFDNWDFLTGYSQSEIEEFALKSFKAIVKKPEGEDQVIHQSSFYLVGPDGKVLKDYNGVENTPYDDIISDVKSASTLK 193
               SCOP domains d1xzob_ B: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SCO1-SenC-1xzoB01 B:3-155                                                                                                                                ------------------- Pfam domains (1)
           Pfam domains (2) SCO1-SenC-1xzoB02 B:3-155                                                                                                                                ------------------- Pfam domains (2)
         Sec.struct. author ........ee....eee.....eee.hhhh...eeeeee...........hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh....hhh.eeee...hhhhhhhhhhhhhh........-.......eeeee....eeeeeee.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----THIOREDOXIN_2  PDB: B:7-172 UniProt: 26-191                                                                                                                           -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xzo B   3 QQIKDPLNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTNCETICPPMTAHMTDLQKKLKAENIDVRIISFSVDPENDKPKQLKKFAANYPLSFDNWDFLTGYSQSEIEEFALKSFKAIVKKPEG-DQVIHQSSFYLVGPDGKVLKDYNGVENTPYDDIISDVKSASTLK 174
                                    12        22        32        42        52        62        72        82        92       102       112       122      |132       142       152       162       172  
                                                                                                                                                        129 |                                           
                                                                                                                                                          131
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XZO)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SCO1_BACSU | P54178)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  1xzo
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 Related Entries

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        SCO1_BACSU | P54178: 1on4

(-) Related Entries Specified in the PDB File

ypmq