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(-) Description

Title :  CRYSTAL STRUCTURE OF UREE FROM HELICOBACTER PYLORI (METAL OF UNKNOWN IDENTITY BOUND)
 
Authors :  R. Shi, C. Munger, A. Assinas, A. Matte, M. Cygler, Montreal-Kingston Structural Genomics Initiative (Bsgi)
Date :  06 Jan 10  (Deposition) - 25 Aug 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Uree In Metal-Bound Form, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Chaperone, Nickel, Nickel Insertion, Virulence, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Shi, C. Munger, A. Asinas, S. L. Benoit, E. Miller, A. Matte, R. J. Maier, M. Cygler
Crystal Structures Of Apo And Metal-Bound Forms Of The Uree Protein From Helicobacter Pylori: Role Of Multiple Metal Binding Sites
Biochemistry V. 49 7080 2010
PubMed-ID: 20681615  |  Reference-DOI: 10.1021/BI100372H

(-) Compounds

Molecule 1 - UREASE ACCESSORY PROTEIN UREE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HP_0070, UREE
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: ATCC 43504

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNX-1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3LA0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LA0)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:13 -Asn A:14
2Leu A:16 -Asp A:17
3Leu B:13 -Asn B:14
4Leu B:16 -Asp B:17
5Leu C:13 -Asn C:14
6Leu C:16 -Asp C:17
7Leu D:13 -Asn D:14
8Leu D:16 -Asp D:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LA0)

(-) Exons   (0, 0)

(no "Exon" information available for 3LA0)

(-) 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:148
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...............eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la0 A   1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la0 B   1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain C from PDB  Type:PROTEIN  Length:147
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           UREE_HELPY     2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la0 C   2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       


Chain D from PDB  Type:PROTEIN  Length:148
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----UreE_N-3la0D05 D:6-71                                             -----UreE_C-3la0D01 D:77-148                                                  Pfam domains (1)
           Pfam domains (2) -----UreE_N-3la0D06 D:6-71                                             -----UreE_C-3la0D02 D:77-148                                                  Pfam domains (2)
           Pfam domains (3) -----UreE_N-3la0D07 D:6-71                                             -----UreE_C-3la0D03 D:77-148                                                  Pfam domains (3)
           Pfam domains (4) -----UreE_N-3la0D08 D:6-71                                             -----UreE_C-3la0D04 D:77-148                                                  Pfam domains (4)
         Sec.struct. author ..................eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la0 D   1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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 3LA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LA0)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: UreE_C] (4)
(-)
Clan: no clan defined [family: UreE_N] (4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (UREE_HELPY | Q09064)
molecular function
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0018307    enzyme active site formation    The modification of part of an enzyme to form the active site.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0019627    urea metabolic process    The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        UREE_HELPY | Q09064: 3l9z 3nxz 3ny0 3tj8 3tj9 3tja

(-) Related Entries Specified in the PDB File

3l9z THE SAME PROTEIN IN APO FORM. RELATED ID: UREE_HELPY RELATED DB: TARGETDB