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(-) Description

Title :  CRYSTAL STRUCTURE OF YRBI LACKING THE LAST 8 RESIDUES, IN COMPLEX WITH KDO AND INORGANIC PHOSPHATE
 
Authors :  T. Biswas, O. V. Tsodikov
Date :  06 Jul 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D,J#
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Yrbi, Kdsc, Kdo, Phosphatase, Hydrolase, Lipopolysaccharide Biosynthesis, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Biswas, L. Yi, P. Aggarwal, J. Wu, J. R. Rubin, J. A. Stuckey, R. W. Woodard, O. V. Tsodikov
The Tail Of Kdsc: Conformational Changes Control The Activity Of A Haloacid Dehalogenase Superfamily Phosphatase
J. Biol. Chem. V. 284 30594 2009
PubMed-ID: 19726684  |  Reference-DOI: 10.1074/JBC.M109.012278

(-) Compounds

Molecule 1 - 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.1.3.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 1-180
    Gene: C3958, KDSC, YRBI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 37762
    Strain: B
    Synonym: KDO 8-P PHOSPHATASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDJ#
Biological Unit 1 (1x): ABCD 
Biological Unit 2 (2x): ABCD 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MG4Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1KDO4Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3PO48Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:34 , ASP A:125 , HOH A:699 , PO4 A:800BINDING SITE FOR RESIDUE MG A 201
02AC2SOFTWAREVAL A:33 , ASP A:34 , THR A:76 , GLY A:77 , LYS A:102 , MG A:201 , HOH A:699 , KDO B:900BINDING SITE FOR RESIDUE PO4 A 800
03AC3SOFTWAREASP B:32 , ASP B:34 , ASP B:125 , PO4 B:800BINDING SITE FOR RESIDUE MG B 202
04AC4SOFTWAREASP B:32 , ASP B:34 , ILE B:75 , THR B:76 , GLY B:77 , LYS B:102 , MG B:202BINDING SITE FOR RESIDUE PO4 B 800
05AC5SOFTWAREASP A:34 , ARG A:78 , PO4 A:800 , ASN B:55 , VAL B:56 , GLY B:59 , ARG B:63 , ARG B:86 , THR B:89 , LEU B:90 , HOH B:513BINDING SITE FOR RESIDUE KDO B 900
06AC6SOFTWAREASP C:32 , ASP C:34 , ASP C:125 , PO4 C:800BINDING SITE FOR RESIDUE MG C 204
07AC7SOFTWAREASP C:32 , VAL C:33 , ASP C:34 , ILE C:75 , THR C:76 , GLY C:77 , LYS C:102 , MG C:204 , KDO D:900BINDING SITE FOR RESIDUE PO4 C 800
08AC8SOFTWAREASP D:32 , ASP D:34 , ASP D:125 , ASP D:129 , PO4 D:800BINDING SITE FOR RESIDUE MG D 203
09AC9SOFTWAREASP D:32 , ASP D:34 , ILE D:75 , THR D:76 , GLY D:77 , LYS D:102 , ILE D:128 , MG D:203BINDING SITE FOR RESIDUE PO4 D 800
10BC1SOFTWAREASP C:34 , ARG C:78 , PO4 C:800 , ASN D:55 , VAL D:56 , ASP D:58 , GLY D:59 , TYR D:60 , ARG D:63 , ARG D:86 , THR D:89 , LEU D:90BINDING SITE FOR RESIDUE KDO D 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I6B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I6B)

(-) Exons   (0, 0)

(no "Exon" information available for 3I6B)

(-) 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:173
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   
           KDSC_ECOL6     7 SLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGK 179
               SCOP domains d3i6ba_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6b A   7 SLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGK 179
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
           KDSC_ECOL6     6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
               SCOP domains d3i6bb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eehhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6b B   6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
           KDSC_ECOL6     6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
               SCOP domains d3i6bc_ C: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eehhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6b C   6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     


Chain D from PDB  Type:PROTEIN  Length:175
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
           KDSC_ECOL6     6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
               SCOP domains d3i6bd_ D: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eehhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6b D   6 ASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I6B)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KDSC_ECOL6 | P67653)
molecular function
    GO:0019143    3-deoxy-manno-octulosonate-8-phosphatase activity    Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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  3.1.3.45
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSC_ECOL6 | P67653: 2r8e 2r8x 2r8y 2r8z 3hyc

(-) Related Entries Specified in the PDB File

2r8e CRYSTAL STRUCTURE OF YRBI FROM ESCHERICHIA COLI IN COMPLEX WITH MG
2r8x CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI
2r8y CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN A COMPLEX WITH CA
2r8z CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH A PHOSPHATE AND A CALCIUM ION
3hyc