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(-) Description

Title :  XANTHOMONAS CAMPESTRIS PUTATIVE OGT (XCC0866), APOSTRUCTURE
 
Authors :  A. W. Schuettelkopf, A. J. Clarke, D. M. F. Van Aalten
Date :  01 May 08  (Deposition) - 18 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Glycosyl Transferase, Gt-B, Ogt, Protein O-Glcnacylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Clarke, R. Hurtado-Guerrero, S. Pathak, A. W. Schuttelkopf, V. Borodkin, S. M. Shepherd, A. F. M. Ibrahim, D. M. F. Van Aalten
Structural Insights Into Mechanism And Specificity Of O-Glcnac Transferase.
Embo J. V. 27 2780 2008
PubMed-ID: 18818698  |  Reference-DOI: 10.1038/EMBOJ.2008.186

(-) Compounds

Molecule 1 - XCC0866
    Atcc: 33913
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 190485

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NHE3Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PR3Ligand/IonPRASEODYMIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PR-1Ligand/IonPRASEODYMIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PR-1Ligand/IonPRASEODYMIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:247 , ASP A:265 , THR A:267 , LEU A:269 , GLU B:364 , PRO B:366 , GLN B:446 , ARG B:450 , HOH B:2167BINDING SITE FOR RESIDUE NHE B1568
2AC2SOFTWAREGLU A:364 , PRO A:365 , PRO A:366 , GLN A:446 , ARG A:450 , HOH A:2119 , HOH A:2151 , HOH A:2152 , ARG B:538 , SER B:540BINDING SITE FOR RESIDUE NHE A1568
3AC3SOFTWARELEU B:269 , HIS B:277 , THR B:358 , TRP B:474 , ARG B:537 , ARG B:538 , PHE B:543 , HIS B:544 , MET B:545 , ASP B:546 , HOH B:2100BINDING SITE FOR RESIDUE NHE B1569
4AC4SOFTWARETRP A:474 , ARG A:537BINDING SITE FOR RESIDUE PEG A1569
5AC5SOFTWAREASP A:455 , PRO A:523 , THR A:527 , HIS A:530 , PR A:1572 , HOH A:2153BINDING SITE FOR RESIDUE PEG A1570
6AC6SOFTWAREGLU A:364 , HOH A:2005 , HOH A:2021 , HOH A:2096BINDING SITE FOR RESIDUE PR A1571
7AC7SOFTWAREASP A:455 , PEG A:1570 , HOH A:2153BINDING SITE FOR RESIDUE PR A1572
8AC8SOFTWAREHIS B:530 , HOH B:2028 , HOH B:2141 , HOH B:2156BINDING SITE FOR RESIDUE PR B1572

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:461 -Pro A:462
2His B:461 -Pro B:462

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VSY)

(-) 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:547
 aligned with Q8PC69_XANCP | Q8PC69 from UniProtKB/TrEMBL  Length:568

    Alignment length:547
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       
         Q8PC69_XANCP    21 QDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRASGVFHMDGFADDFGALLQALARRHGWLG 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhh...............eeeeeee.....hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhh.eeee....hhhhhhhhhhhh...eeee.........hhhhhh....eeeee.............eeee........hhhhh..eeee...................hhhhh......eeee..hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh..hhh.eeee...hhhhhhhhhhhh.eee.......hhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsy A  21 QDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRASGVFHMDGFADDFGALLQALARRHGWLG 567
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       


Chain B from PDB  Type:PROTEIN  Length:547
 aligned with Q8PC69_XANCP | Q8PC69 from UniProtKB/TrEMBL  Length:568

    Alignment length:547
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       
         Q8PC69_XANCP    21 QDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRASGVFHMDGFADDFGALLQALARRHGWLG 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------TPR_11-2vsyB05 B:55-122                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyco_transf_41-2vsyB01 B:360-560                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ----------------------------------TPR_11-2vsyB06 B:55-122                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyco_transf_41-2vsyB02 B:360-560                                                                                                                                                                        ------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyco_transf_41-2vsyB03 B:360-560                                                                                                                                                                        ------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyco_transf_41-2vsyB04 B:360-560                                                                                                                                                                        ------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhh...............eeeeeee.....hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhheeee....hhhhhhhhhhhh...eeee.........hhhhhh....eeeee.............eeee.....hhhhhhhh..eeee.............................eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..hhh.eeee...hhhhhhhhhhhh.eee.......hhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsy B  21 QDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRASGVFHMDGFADDFGALLQALARRHGWLG 567
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560
   Legend:   → Mismatch (orange background)
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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 2VSY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: GT-B (132)
(-)
Clan: TPR (230)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8PC69_XANCP | Q8PC69)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2vsy
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 Related Entries

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

UniProtKB/TrEMBL
        Q8PC69_XANCP | Q8PC69: 2jlb 2xgm 2xgo 2xgs

(-) Related Entries Specified in the PDB File

2jlb XANTHOMONAS CAMPESTRIS PUTATIVE OGT (XCC0866), COMPLEX WITH UDP-GLCNAC PHOSPHONATE ANALOGUE