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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI YIIL PROTEIN CONTAINING L-RHAMNOSE
 
Authors :  K. S. Ryu, J. I. Kim, S. J. Cho, D. Park, C. Park, J. O. Lee, B. S. Choi
Date :  18 Aug 04  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Mutarotase, L-Rhamnose, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Ryu, J. I. Kim, S. J. Cho, D. Park, C. Park, H. K. Cheong, J. O. Lee, B. S. Choi
Structural Insights Into The Monosaccharide Specificity Of Escherichia Coli Rhamnose Mutarotase
J. Mol. Biol. V. 349 153 2005
PubMed-ID: 15876375  |  Reference-DOI: 10.1016/J.JMB.2005.03.047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YIIL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: L-RHAMNOSE MUTAROTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1RNS4Ligand/IonL-RHAMNOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1RNS2Ligand/IonL-RHAMNOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1RNS2Ligand/IonL-RHAMNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:18 , HIS A:22 , TYR A:41 , TRP A:76 , TRP A:77 , HOH A:1118 , HOH A:1129 , HOH A:1179BINDING SITE FOR RESIDUE RNS A 1105
2AC2SOFTWARETYR B:18 , HIS B:22 , TYR B:41 , TRP B:76 , TRP B:77 , HOH B:1109 , HOH B:1168BINDING SITE FOR RESIDUE RNS B 1106
3AC3SOFTWARETYR C:18 , HIS C:22 , LEU C:29 , TYR C:41 , TRP C:76 , TRP C:77 , HOH C:1108 , HOH C:1207 , HOH C:1226BINDING SITE FOR RESIDUE RNS C 1107
4AC4SOFTWARETYR D:18 , HIS D:22 , LEU D:29 , TYR D:41 , TRP D:76 , TRP D:77 , HOH D:1128 , HOH D:1140 , HOH D:1234BINDING SITE FOR RESIDUE RNS D 1108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X8D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:23 -Pro A:24
2Asn B:23 -Pro B:24
3Asn C:23 -Pro C:24
4Asn D:23 -Pro D:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X8D)

(-) Exons   (0, 0)

(no "Exon" information available for 1X8D)

(-) 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:104
 aligned with RHAM_ECOLI | P32156 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           RHAM_ECOLI     1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
               SCOP domains d1x8da1 A:1-104 L-rhamnose mutarotase YiiL                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhh....hhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhh..hhhhhhhhhhhh............eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1x8d A   1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with RHAM_ECOLI | P32156 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           RHAM_ECOLI     1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
               SCOP domains d1x8db_ B: L-rhamnose mutarotase YiiL                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhh....hhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhh..hhhhhhhhhhhh............eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1x8d B   1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain C from PDB  Type:PROTEIN  Length:104
 aligned with RHAM_ECOLI | P32156 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           RHAM_ECOLI     1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
               SCOP domains d1x8dc_ C: L-rhamnose mutarotase YiiL                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhh...hhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhhh.hhhhhhhhhhhh............eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1x8d C   1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with RHAM_ECOLI | P32156 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           RHAM_ECOLI     1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
               SCOP domains d1x8dd_ D: L-rhamnose mutarotase YiiL                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -DUF718-1x8dD01 D:2-104                                                                                  Pfam domains (1)
           Pfam domains (2) -DUF718-1x8dD02 D:2-104                                                                                  Pfam domains (2)
           Pfam domains (3) -DUF718-1x8dD03 D:2-104                                                                                  Pfam domains (3)
           Pfam domains (4) -DUF718-1x8dD04 D:2-104                                                                                  Pfam domains (4)
         Sec.struct. author .eeeeeeee....hhhhhhhhh...hhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhh..hhhhhhhhhhhh............eee.eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1x8d D   1 MIRKAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMTDVMPANPDNSPVSSELQEVFYLP 104
                                    10        20        30        40        50        60        70        80        90       100
   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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X8D)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Dim_A_B_barrel (36)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RHAM_ECOLI | P32156)
molecular function
    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:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019301    rhamnose catabolic process    The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
    GO:0019299    rhamnose metabolic process    The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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