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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN AGX2 COMPLEXED WITH UDPGLCNAC
 
Authors :  C. Peneff, Y. Bourne
Date :  29 Aug 01  (Deposition) - 29 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleotidyltransferase, Alternative Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Peneff, P. Ferrari, V. Charrier, Y. Taburet, C. Monnier, V. Zamboni, J. Winter, M. Harnois, F. Fassy, Y. Bourne
Crystal Structures Of Two Human Pyrophosphorylase Isoforms In Complexes With Udpglc(Gal)Nac: Role Of The Alternatively Spliced Insert In The Enzyme Oligomeric Assembly And Active Site Architecture.
Embo J. V. 20 6191 2001
PubMed-ID: 11707391  |  Reference-DOI: 10.1093/EMBOJ/20.22.6191
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDPGLCNAC PYROPHOSPHORYLASE (AGX2)
    ChainsA, B
    EC Number2.7.7.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRU277
    Expression System StrainXL1 BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAGX2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:108 , ALA A:109 , GLY A:110 , MET A:165 , GLN A:196 , PRO A:220 , GLY A:222 , ASN A:223 , CYS A:251 , VAL A:252 , VAL A:289 , GLY A:290 , GLU A:303 , TYR A:304 , ASN A:327 , PHE A:381 , PHE A:383 , PHE A:403 , LYS A:407 , HOH A:931 , HOH A:972 , HOH A:1020 , ARG B:453BINDING SITE FOR RESIDUE UD1 A 901
2AC2SOFTWAREARG A:453 , LEU B:108 , ALA B:109 , GLY B:110 , GLY B:111 , MET B:165 , GLN B:196 , PRO B:220 , GLY B:222 , ASN B:223 , CYS B:251 , VAL B:252 , VAL B:289 , GLY B:290 , GLU B:303 , TYR B:304 , ASN B:327 , PHE B:381 , PHE B:383 , PHE B:403 , LYS B:407 , HOH B:916 , HOH B:939 , HOH B:1019BINDING SITE FOR RESIDUE UD1 B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:477 -Pro A:478
2Ala A:505 -Pro A:506
3Ala B:505 -Pro B:506

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014935P418HUAP1_HUMANPolymorphism1128539A/BP418H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (10, 20)

Asymmetric/Biological Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000003679253bENSE00001445937chr1:162535827-162536138312UAP1_HUMAN1-94942A:2-94 (gaps)
B:2-94 (gaps)
93
93
1.4ENST000003679254ENSE00000958805chr1:162546567-162546771205UAP1_HUMAN94-162692A:94-162 (gaps)
B:94-162 (gaps)
69
69
1.5bENST000003679255bENSE00000958806chr1:162549218-162549393176UAP1_HUMAN162-221602A:162-221
B:162-221
60
60
1.6aENST000003679256aENSE00000958807chr1:162551077-162551249173UAP1_HUMAN221-278582A:221-278
B:221-278
58
58
1.7aENST000003679257aENSE00000958808chr1:162557265-162557458194UAP1_HUMAN279-343652A:279-343
B:279-343
65
65
1.8ENST000003679258ENSE00000958809chr1:162558483-162558623141UAP1_HUMAN343-390482A:343-390
B:343-390
48
48
1.9ENST000003679259ENSE00000958810chr1:162560113-162560301189UAP1_HUMAN390-453642A:390-453
B:390-453
64
64
1.10aENST0000036792510aENSE00000958811chr1:162562522-16256257251UAP1_HUMAN453-470182A:453-456
B:453-453
4
1
1.11bENST0000036792511bENSE00000958812chr1:162567582-16256764867UAP1_HUMAN470-492232A:477-492
B:477-492
16
16
1.12bENST0000036792512bENSE00001445936chr1:162569061-162569621561UAP1_HUMAN493-522302A:493-517
B:493-518
25
26

(-) Sequences/Alignments

Asymmetric/Biological 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:480
 aligned with UAP1_HUMAN | Q16222 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:516
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511      
           UAP1_HUMAN     2 NINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQSSHQKNVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSATNGKSETITADVNHNLKDANDVPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHEL 517
               SCOP domains d1jvda_ A: UDP-N-acetylglucosamine pyrophosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1jvdA01 A:2-437 Spore Coat Polysaccharide Biosynthesis            Protein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                             -------------------                    ----------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.-----------.ee..hhh.eee......hhhhhhhhhhhhhhh..eeeeeee...-----...hhhhh........hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..eee.ee......eee..ee.eee.hhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhh...eeeeeee.........eeeee..eeeeehhhhhhhhhhh...........eeeeeeeeeehhhhhhhhhhhhhhh..eeeee...ee.....ee......eeeee.hhhhhhhhh..eeeee.hhhhhh.............hhhhhhhhhhhhhhhhhhhh..ee................--------------------....eee..........hhhhhh..ee...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:2-94 (gaps) UniProt: 1-94 [INCOMPLETE]                                     -------------------------------------------------------------------Exon 1.5b  PDB: A:162-221 UniProt: 162-221                  ---------------------------------------------------------Exon 1.7a  PDB: A:279-343 UniProt: 279-343                       -------------------------------------------------------------------------------------------------------------Exon 1.10a        ----------------------Exon 1.12b  PDB: A:493-51 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.4  PDB: A:94-162 (gaps) UniProt: 94-162                       ----------------------------------------------------------Exon 1.6a  PDB: A:221-278 UniProt: 221-278                ----------------------------------------------------------------Exon 1.8  PDB: A:343-390 UniProt: 343-390       -------------------------------------------------------------------------------Exon 1.11b [INCOMPLETE]------------------------- Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:390-453 UniProt: 390-453                       ---------------------------------------------------------------- Transcript 1 (3)
                 1jvd A   2 NINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGF-----------RMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQ-----VAYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSAT--------------------VPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHEL 517
                                    11        21        31        41        51    |    -      | 71        81        91       101       111|     |121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    |    -         -     | 481       491       501       511      
                                                                                 56          68                                         112   118                                                                                                                                                                                                                                                                                                                                               456                  477                                        

Chain B from PDB  Type:PROTEIN  Length:486
 aligned with UAP1_HUMAN | Q16222 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:517
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       
           UAP1_HUMAN     2 NINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQSSHQKNVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSATNGKSETITADVNHNLKDANDVPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHELV 518
               SCOP domains d1jvdb_ B: UDP-N-acetylglucosamine pyrophosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1jvdB01 B:2-437 Spore Coat Polysaccharide Biosynthesis Pr     otein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                                   ----------------                       ------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------UDPGP-1jvdB01 B     :44-453                                                                                                                                                                                                                                                                                                                                                                                                                      ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------UDPGP-1jvdB02 B     :44-453                                                                                                                                                                                                                                                                                                                                                                                                                      ------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...-----hhhhhee..hhh.eee...hhhhhhhhhhhhhhhhhh..eeeeee.......---..hhhhh........hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..eee.ee......eee..ee.eee.hhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhh...eeeeeee.........eeeee..eeeeehhhhhhhhhhhh..........eeeeeeeeeehhhhhhhhhhhhhhh..eeeee...ee.....ee......eeeee.hhhhhhhhh..eeeeeehhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhh..ee.............-----------------------....eee..........hhhhhh..ee...eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:2-94 (gaps) UniProt: 1-94 [INCOMPLETE]                                     -------------------------------------------------------------------Exon 1.5b  PDB: B:162-221 UniProt: 162-221                  ---------------------------------------------------------Exon 1.7a  PDB: B:279-343 UniProt: 279-343                       -------------------------------------------------------------------------------------------------------------Exon 1.10a        ----------------------Exon 1.12b  PDB: B:493-518 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.4  PDB: B:94-162 (gaps) UniProt: 94-162                       ----------------------------------------------------------Exon 1.6a  PDB: B:221-278 UniProt: 221-278                ----------------------------------------------------------------Exon 1.8  PDB: B:343-390 UniProt: 343-390       -------------------------------------------------------------------------------Exon 1.11b [INCOMPLETE]-------------------------- Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:390-453 UniProt: 390-453                       ----------------------------------------------------------------- Transcript 1 (3)
                 1jvd B   2 NINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQ-----NVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTR---AYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPR-----------------------VPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHELV 518
                                    11        21        31        41        51      |  -  |     71        81        91       101       111   |   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451 |       -         -     | 481       491       501       511       
                                                                                   58    64                                                115 119                                                                                                                                                                                                                                                                                                                                           453                     477                                         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UAP1_HUMAN | Q16222)
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:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006047    UDP-N-acetylglucosamine metabolic process    The chemical reactions and pathways involving 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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UAP1_HUMAN | Q162221jv1 1jv3 1jvg

(-) Related Entries Specified in the PDB File

1jv1 STRUCTURE OF AGX1 COMPLEXED WITH UDPGLCNAC
1jv3 STRUCTURE OF AGX1 COMPLEXED WITH UDPGALNAC
1jvg STRUCTURE OF AGX2 COMPLEXED WITH UDPGALNAC