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(-) Description

Title :  CRYSTAL STRUCTURE OF URIDINE-DIPHOSPHO-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE FROM CANDIDA ALBICANS, IN THE REACTION-COMPLETED FORM
 
Authors :  K. Miki, D. Maruyama, Y. Nishitani, T. Nonaka, A. Kita
Date :  30 Mar 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pyrophosphorylase, N-Acetylglucosamine, Uridine-Diphospho-N- Acetylglucosamine, Candida Albicans, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Maruyama, Y. Nishitani, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, K. Miki
Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine Pyrophosphorylase From Candida Albicans And Catalytic Reaction Mechanism
J. Biol. Chem. V. 282 17221 2007
PubMed-ID: 17392279  |  Reference-DOI: 10.1074/JBC.M611873200

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.7.7.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476

 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, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION
4UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
4UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
4UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:114 , THR A:115 , ARG A:116 , UD1 A:1001BINDING SITE FOR RESIDUE SO4 A 1101
2AC2SOFTWAREARG A:285 , LYS A:328 , ARG A:332 , HOH A:1415BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWAREASN A:74 , THR A:77 , HOH A:1445BINDING SITE FOR RESIDUE MG A 1201
4AC4SOFTWARELYS B:328 , ARG B:332BINDING SITE FOR RESIDUE SO4 B 2102
5AC5SOFTWAREMET A:109 , GLY A:111 , GLY A:112 , ARG A:116 , MET A:168 , GLN A:199 , PRO A:224 , GLY A:226 , ASN A:227 , CYS A:255 , VAL A:256 , VAL A:293 , GLY A:294 , GLU A:309 , TYR A:310 , ASN A:335 , VAL A:337 , PHE A:393 , PHE A:395 , PHE A:417 , LYS A:421 , SO4 A:1101 , HOH A:1366 , HOH A:1386 , HOH A:1389 , HOH A:1402 , HOH A:1404 , HOH A:1439BINDING SITE FOR RESIDUE UD1 A 1001
6AC6SOFTWAREMET B:109 , GLY B:111 , GLY B:112 , ARG B:116 , MET B:168 , GLN B:199 , PRO B:224 , GLY B:226 , ASN B:227 , CYS B:255 , VAL B:256 , ASP B:257 , VAL B:293 , GLY B:294 , GLU B:309 , TYR B:310 , ASN B:335 , VAL B:337 , PHE B:393 , PHE B:395 , PHE B:417 , LYS B:421 , HOH B:2114 , HOH B:2119 , HOH B:2171 , HOH B:2175BINDING SITE FOR RESIDUE UD1 B 2001
7AC7SOFTWAREPHE A:196 , ASN A:237 , HOH A:1313 , HOH A:1377 , GLN B:6 , HOH B:2174BINDING SITE FOR RESIDUE GOL A 1301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:204 -A:221
2B:204 -B:221

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YQJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YQJ)

(-) 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:473
 aligned with UAP1_CANAX | O74933 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:484
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    
           UAP1_CANAX     3 VKSQQQIIDSFKQANQDQLFQYYDSLTIDQQQEFIDQLSTIEEPAKLISTVEQAIQFSQTNSTSRNFTQLPNEQTASTLDLSKDILQNWTELGLKAIGNGEVAVLLMAGGQGTRLGSSAPKGCFNIELPSQKSLFQIQAEKILKIEQLAQQYLKSTKKPIINWYIMTSGPTRNATESFFIENNYFGLNSHQVIFFNQGTLPCFNLQGNKILLESKNSICQSPDGNGGLYKALKDNGILDDLNSKGIKHIHMYCVDNCLVKVADPIFIGFAIAKKFDLATKVVRKRDANESVGLIVLDQDNQKPCVIEYSEISQELANKKDPQDSSKLFLRAANIVNHYYSVEFLNKMIPKWISSQKYLPFHIAKKKIPSLNLENGEFYKPTEPNGIKLEQFIFDVFPSVELNKFGCLEVDRLDEFSPLKNADGAKNDTPTTCRNHYLERSSKWVIQNGGVIDNQGLVEVDSKTSYGGEGLEFVNGKHFKNGDII 486
               SCOP domains d2yqja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2yqjA01 A:3-450 Spore Coat Polysaccharide Biosynthesis          Protein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                                           ------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh---------..ee..hhh.eee....hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhh...hhhhh........hhhhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..eee.ee.......eee..ee.eee.hhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhh..eeeeeee.........eeeee....eeeee.....hhhhhh.ee..eeeee...eeeeeeeeeehhhhhhhhhhhh........eeeee.......--..........eeeee.hhhhhhhhhhhh.eeeee.hhhhhh............hhhhhhhhhhhhhhhhhhhh..ee..................hhhhh..ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yqj A   3 VKSQQQIIDSFKQANQDQLFQYYDSLTIDQQQEFIDQLSTIEEPAKLISTVEQAI---------RNFTQLPNEQTASTLDLSKDILQNWTELGLKAIGNGEVAVLLMAGGQGTRLGSSAPKGCFNIELPSQKSLFQIQAEKILKIEQLAQQYLKSTKKPIINWYIMTSGPTRNATESFFIENNYFGLNSHQVIFFNQGTLPCFNLQGNKILLELKNSICQSPDGNGGLYKALKDNGILDDLNSKGIKHIHMYCVDNCLVKVADPIFIGFAIAKKFDLATKVVRKRDANESVGLIVLDQDNQKPCVIEYSEISQELANKKDPQDSSKLFLRAANIVNHYYSVEFLNKMIPKWISSQKYLPFHIAKKKIPSLNL--GEFYKPTEPNGIKLEQFIFDVFPSVELNKFGCLEVDRLDEFSPLKNADGAKNDTPTTCRNHYLERSSKWVIQNGGVIDNQGLVEVDSKTSYGGEGLEFVNGKHFKNGDII 486
                                    12        22        32        42        52    |    -    |   72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 |  |  382       392       402       412       422       432       442       452       462       472       482    
                                                                                 57        67                                                                                                                                                                                                                                                                                                                374  |                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                377                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:471
 aligned with UAP1_CANAX | O74933 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:484
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    
           UAP1_CANAX     3 VKSQQQIIDSFKQANQDQLFQYYDSLTIDQQQEFIDQLSTIEEPAKLISTVEQAIQFSQTNSTSRNFTQLPNEQTASTLDLSKDILQNWTELGLKAIGNGEVAVLLMAGGQGTRLGSSAPKGCFNIELPSQKSLFQIQAEKILKIEQLAQQYLKSTKKPIINWYIMTSGPTRNATESFFIENNYFGLNSHQVIFFNQGTLPCFNLQGNKILLESKNSICQSPDGNGGLYKALKDNGILDDLNSKGIKHIHMYCVDNCLVKVADPIFIGFAIAKKFDLATKVVRKRDANESVGLIVLDQDNQKPCVIEYSEISQELANKKDPQDSSKLFLRAANIVNHYYSVEFLNKMIPKWISSQKYLPFHIAKKKIPSLNLENGEFYKPTEPNGIKLEQFIFDVFPSVELNKFGCLEVDRLDEFSPLKNADGAKNDTPTTCRNHYLERSSKWVIQNGGVIDNQGLVEVDSKTSYGGEGLEFVNGKHFKNGDII 486
               SCOP domains d2yqjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2yqjB01 B:3-450 Spore Coat Polysaccharide Biosynthesis           Protein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                                          ------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh----------..ee..hhh.eee....hhhhhhhhhhhhhhhhhh..eeeeee............hhhhh........hhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhhhhhhh.eeeee..eee..........eee..ee.eee.hhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhh..eeeeeee.........eeeee....eeeee.....hhhhhhhee..eeeee...eeeeeeeeeehhhhhhhhhhhhh.......eeeee...ee..---.ee......eeeee.hhhhhhhhhhhh.eeeee.hhhhhh............hhhhhhhhhhhhhhhhhhhh..ee.hhh..............hhhhh..ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yqj B   3 VKSQQQIIDSFKQANQDQLFQYYDSLTIDQQQEFIDQLSTIEEPAKLISTVEQA----------RNFTQLPNEQTASTLDLSKDILQNWTELGLKAIGNGEVAVLLMAGGQGTRLGSSAPKGCFNIELPSQKSLFQIQAEKILKIEQLAQQYLKSTKKPIINWYIMTSGPTRNATESFFIENNYFGLNSHQVIFFNQGTLPCFNLQGNKILLELKNSICQSPDGNGGLYKALKDNGILDDLNSKGIKHIHMYCVDNCLVKVADPIFIGFAIAKKFDLATKVVRKRDANESVGLIVLDQDNQKPCVIEYSEISQELANKKDPQDSSKLFLRAANIVNHYYSVEFLNKMIPKWISSQKYLPFHIAKKKIPSLNL---EFYKPTEPNGIKLEQFIFDVFPSVELNKFGCLEVDRLDEFSPLKNADGAKNDTPTTCRNHYLERSSKWVIQNGGVIDNQGLVEVDSKTSYGGEGLEFVNGKHFKNGDII 486
                                    12        22        32        42        52   |     -    |   72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 |   | 382       392       402       412       422       432       442       452       462       472       482    
                                                                                56         67                                                                                                                                                                                                                                                                                                                374 378
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YQJ)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UAP1_CANAX | O74933)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0070569    uridylyltransferase activity    Catalysis of the transfer of an uridylyl group to an acceptor.
biological process
    GO:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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
        UAP1_CANAX | O74933: 2yqc 2yqh 2yqs

(-) Related Entries Specified in the PDB File

2yqc THE SAME PROTEIN IN THE APO-LIKE FORM
2yqh THE SAME PROTEIN IN THE SUBSTRATE-BINDING FORM
2yqs THE SAME PROTEIN IN THE PRODUCT-BINDING FORM