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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE (AGX2) FROM MUS MUSCULUS AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  10 Sep 04  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Agx2, 16741099, Udp-N-Acetylglucosamine Pyrophosphorylase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Udp-N-Acetylglucosamine Pyrophosphorylase (Agx2) From Mus Musculus At 2. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.7.7.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 33)

Asymmetric/Biological Unit (3, 33)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:9 , ASN B:41 , PHE B:42BINDING SITE FOR RESIDUE CL B 523
2AC2SOFTWAREARG B:422 , HIS B:423BINDING SITE FOR RESIDUE CL B 524
3AC3SOFTWARELYS B:180BINDING SITE FOR RESIDUE CL B 525
4AC4SOFTWAREGLU B:502 , HOH B:552BINDING SITE FOR RESIDUE CL B 526
5AC5SOFTWAREARG A:9 , PHE A:42BINDING SITE FOR RESIDUE CL A 523
6AC6SOFTWARELYS B:390BINDING SITE FOR RESIDUE EDO B 527
7AC7SOFTWARELEU B:77 , ASP B:83 , LYS B:271 , HOH B:584BINDING SITE FOR RESIDUE EDO B 528

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VM8)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_UAP1_MOUSE_001 *Y366HUAP1_MOUSE  ---  ---A/BY366H
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VM8)

(-) Exons   (0, 0)

(no "Exon" information available for 1VM8)

(-) 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:491
 aligned with UAP1_MOUSE | Q91YN5 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_MOUSE     2 NVNDLKQRLSQAGQEHLLQFWNELSEAQQVELYMELQAMNFEELNSFFRKAIGEFDRSSHQEKVDARMEPVPRQVLGSATRDQEQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVSYPKGMYDVGLPSHKTLFQIQAERILKLQQLAEKHHGNKCTIPWYIMTSGRTMESTKEFFTKHKFFGLKKENVVFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGICSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQRRSSDGRLLFNAGNIANHFFTVPFLKDVVNVYEPQLQHHVAQKKIPYVDSQGYFIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSATNGKSEAITADVNHNLKDANDVPIQCEISPLISYAGEGLEGYVADKEFHAPLIIDENGVHEL 517
               SCOP domains d1vm8a_ A: UDP-N-acetylglucosamine pyrophosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1vm8A01 A:2-437 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                                        ---------------                        ----------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhh.ee..hhh.eee.....hhhhhhhhhhhhhhhh..eeeeee............hhhhh........hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..eee.ee......eee..ee.eee...hhhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhh...eeeeeee.........eeeee..eeeee.....hhhhhhh..........eeeeeeeeeehhhhhhhhhhhhhhh..eeeee...ee.....ee......eeeee.hhhhhhhhh..eeeeeehhhhhh.........-...hhhhhhhhhhhhhhhhhhhh.eee............------------------------....eee..........hhhhhh.eee...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vm8 A   2 NVNDLKQRLSQAGQEHLLQFWNELSEAQQmELYmELQAmNFEELNSFFRKAIGEFDRSSHQEKVDARmEPVPRQVLGSATRDQEQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVSYPKGmYDVGLPSHKTLFQIQAERILKLQQLAEKHHGNKCTIPWYImTSGRTmESTKEFFTKHKFFGLKKENVVFFQQGmLPAmSFDGKIILEEKNKVSmAPDGNGGLYRALAAQNIVEDmEQRGICSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQRRSSDGRLLFNAGNIANHFFTVPFLKDVVNVYEPQLQHHVAQKKIPYVDSQGYFIKPDKPNGIKmEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQ-GKDNPTTARHALmSLHHCWVLNAGGHFIDENGSRLPAIP------------------------VPIQCEISPLISYAGEGLEGYVADKEFHAPLIIDENGVHEL 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|        -         -     | 481       491       501       511      
                                                        31-MSE    |                           69-MSE                                                124-MSE                                  165-MSE |                        198-MSE             218-MSE              239-MSE                                                                                                                                    378-MSE                           412 |         426-MSE                   452                      477                                        
                                                            35-MSE|                                                                                                                                171-MSE                        202-MSE                                                                                                                                                                                                             414                                                                                                       
                                                                 40-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:490
 aligned with UAP1_MOUSE | Q91YN5 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:515
                                    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_MOUSE     2 NVNDLKQRLSQAGQEHLLQFWNELSEAQQVELYMELQAMNFEELNSFFRKAIGEFDRSSHQEKVDARMEPVPRQVLGSATRDQEQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVSYPKGMYDVGLPSHKTLFQIQAERILKLQQLAEKHHGNKCTIPWYIMTSGRTMESTKEFFTKHKFFGLKKENVVFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGICSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQRRSSDGRLLFNAGNIANHFFTVPFLKDVVNVYEPQLQHHVAQKKIPYVDSQGYFIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSATNGKSEAITADVNHNLKDANDVPIQCEISPLISYAGEGLEGYVADKEFHAPLIIDENGVHE 516
               SCOP domains d1vm8b_ B: UDP-N-acetylglucosamine pyrophosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1vm8B01 B:2-437 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                                                                                                                                                                        ----------------                       ---------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------UDPGP-1vm8B01 B:44-453                                                                                                                                                                                                                                                                                                                                                                                                                           ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------UDPGP-1vm8B02 B:44-453                                                                                                                                                                                                                                                                                                                                                                                                                           ---------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhh.ee..hhh.eee......hhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhhh.eeeee..eee.ee......eee..ee.eee...hhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhh...eeeeeee.........eeeee..eeeeehhhhhhhhhhhh..........eeeeeeeeeehhhhhhhhhh.......eeeee...ee.....ee......eeeee.hhhhhhhhh..eeeeeehhhhhh........--...hhhhhhhhhhhhhhhhhhhh..ee.............-----------------------....eee..........hhhhhh..ee...eeee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vm8 B   2 NVNDLKQRLSQAGQEHLLQFWNELSEAQQmELYmELQAmNFEELNSFFRKAIGEFDRSSHQEKVDARmEPVPRQVLGSATRDQEQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVSYPKGmYDVGLPSHKTLFQIQAERILKLQQLAEKHHGNKCTIPWYImTSGRTmESTKEFFTKHKFFGLKKENVVFFQQGmLPAmSFDGKIILEEKNKVSmAPDGNGGLYRALAAQNIVEDmEQRGICSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQRRSSDGRLLFNAGNIANHFFTVPFLKDVVNVYEPQLQHHVAQKKIPYVDSQGYFIKPDKPNGIKmEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADS--GKDNPTTARHALmSLHHCWVLNAGGHFIDENGSRLPAIPR-----------------------VPIQCEISPLISYAGEGLEGYVADKEFHAPLIIDENGVHE 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 |       -         -     | 481       491       501       511     
                                                        31-MSE    |                           69-MSE                                                124-MSE                                  165-MSE |                        198-MSE             218-MSE              239-MSE                                                                                                                                    378-MSE                          411  |         426-MSE                    453                     477                                       
                                                            35-MSE|                                                                                                                                171-MSE                        202-MSE                                                                                                                                                                                                             414                                                                                                      
                                                                 40-MSE
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UAP1_MOUSE | Q91YN5)
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: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: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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  1vm8
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 Related Entries

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