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(-) Description

Title :  THE UDP COMPLEX STRUCTURE OF THE SIXTH GENE PRODUCT OF THE F1-ATPASE OPERON OF RHODOBACTER BLASTICUS
 
Authors :  C. Enroth, A. Strid
Date :  29 Jun 07  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Majastridin, Atpase Operon, Glycosyl Transferase, Rossmann Fold, Udp- Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Enroth, A. Strid
Crystal Structure Of A Protein, Structurally Related To Glycosyltransferases, Encoded In The Rhodobacter Blasticus Atp Operon.
Biochim. Biophys. Acta V. 1784 379 2008
PubMed-ID: 18067873  |  Reference-DOI: 10.1016/J.BBAPAP.2007.11.005

(-) Compounds

Molecule 1 - ATP SYNTHASE SUBUNITS REGION ORF 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Organism Scientific: RHODOBACTER BLASTICUS
    Organism Taxid: 1075

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:82 , ASP A:84 , HIS A:202 , HOH A:429 , HOH A:435BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREHIS B:82 , ASP B:84 , HIS B:202 , UDP B:800BINDING SITE FOR RESIDUE MN B 300
3AC3SOFTWARELEU B:23 , ARG B:25 , ASN B:54 , ASN B:58 , HIS B:82 , GLU B:83 , ASP B:84 , PHE B:175 , HIS B:202 , GLY B:204 , ARG B:205 , MN B:300 , HOH B:803 , HOH B:804 , HOH B:807 , HOH B:1119 , HOH B:1145BINDING SITE FOR RESIDUE UDP B 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:146 -Pro A:147
2Val B:146 -Pro B:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QGI)

(-) 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:248
 aligned with YAT6_RHOBL | P05449 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           YAT6_RHOBL     2 KPVPTYVQDKDESTLMFSVCSLVRDQAKYDRLLESFERFGFTPDKAEFLAADNREGNQFHGFSWHKQMLPRCKGRYVIFCHEDVELVDRGYDDLVAAIEALEEADPKWLVAGVAGSPWRPLNHSVTAQALHISDVFGNDRRRGNVPCRVESLDECFLLMRRLKPVLNSYDMQGFHYYGADLCLQAEFLGGRAYAIDFHLHHYGRAIADENFHRLRQEMAQKYRRWFPGRILHCVTGRVALGGGWYEAR 249
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.........eeeeeee.hhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhh...eeeeee..ee....hhhhhhhhhhhhhhhh..eeeee.eeee...........eeeeee..eeeeee....eeeeee...eeeee...............hhhhhhhhhhhhh..eeee.....ee......hhhhhhhhhhhhhhhh......eeee..eeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qgi A   2 KPVPTYVQDKDESTLMFSVCSLVRDQAKYDRLLESFERFGFTPDKAEFLAADNREGNQFHGFSWHKQMLPRCKGRYVIFCHEDVELVDRGYDDLVAAIEALEEADPKWLVAGVAGSPWRPLNHSVTAQALHISDVFGNDRRRGNVPCRVESLDECFLLMRRLKPVLNSYDMQGFHYYGADLCLQAEFLGGRAYAIDFHLHHYGRAIADENFHRLRQEMAQKYRRWFPGRILHCVTGRVALGGGWYEAR 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with YAT6_RHOBL | P05449 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           YAT6_RHOBL     2 KPVPTYVQDKDESTLMFSVCSLVRDQAKYDRLLESFERFGFTPDKAEFLAADNREGNQFHGFSWHKQMLPRCKGRYVIFCHEDVELVDRGYDDLVAAIEALEEADPKWLVAGVAGSPWRPLNHSVTAQALHISDVFGNDRRRGNVPCRVESLDECFLLMRRLKPVLNSYDMQGFHYYGADLCLQAEFLGGRAYAIDFHLHHYGRAIADENFHRLRQEMAQKYRRWFPGRILHCVTGRVALGGGWYEAR 249
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------Glyco_tranf_2_5-2qgiB01 B:18-223                                                                                                                                                                              -------------------------- Pfam domains (1)
           Pfam domains (2) ----------------Glyco_tranf_2_5-2qgiB02 B:18-223                                                                                                                                                                              -------------------------- Pfam domains (2)
         Sec.struct. author ....eee.........eeeeeee.hhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhh...eeeeee..ee....hhhhhhhhhhhhhhhh..eeeee.eeee...........eeeeee..eeeeee....eeeeee...eeeee...............hhhhhhhhhhhhh..eeee.....ee......hhhhhhhhhhhhhhhh......eeee..eeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qgi B   2 KPVPTYVQDKDESTLMFSVCSLVRDQAKYDRLLESFERFGFTPDKAEFLAADNREGNQFHGFSWHKQMLPRCKGRYVIFCHEDVELVDRGYDDLVAAIEALEEADPKWLVAGVAGSPWRPLNHSVTAQALHISDVFGNDRRRGNVPCRVESLDECFLLMRRLKPVLNSYDMQGFHYYGADLCLQAEFLGGRAYAIDFHLHHYGRAIADENFHRLRQEMAQKYRRWFPGRILHCVTGRVALGGGWYEAR 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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  (0, 0)

(no "SCOP Domain" information available for 2QGI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2QGI)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        YAT6_RHOBL | P05449: 2nxv

(-) Related Entries Specified in the PDB File

2nxv THE STRUCTURE OF THE APO FORM OF THE SAME PROTEIN WITHOUT UDP