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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN GLUTAMINYL CYCLASE MUTANT S160G AT 1.99 ANGSTROM RESOLUTION
 
Authors :  K. F. Huang, Y. R. Wang, E. C. Chang, T. L. Chou, A. H. Wang
Date :  12 Dec 07  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (3x)
Keywords :  Hydrogen Bond Network, Glutaminyl Cyclase, Pyroglutamate, Site- Directed Mutagenesis, Proton Transfer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. F. Huang, Y. R. Wang, E. C. Chang, T. L. Chou, A. H. Wang
A Conserved Hydrogen-Bond Network In The Catalytic Centre O Animal Glutaminyl Cyclases Is Critical For Catalysis.
Biochem. J. V. 411 181 2008
PubMed-ID: 18072935  |  Reference-DOI: 10.1042/BJ20071073

(-) Compounds

Molecule 1 - GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE
    ChainsA, B
    EC Number2.3.2.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET32A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 33-361
    GeneQPCT
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymQC, GLUTAMINYL-TRNA CYCLOTRANSFERASE, GLUTAMINYL CYCLASE, GLUTAMYL CYCLASE
    TissueBONE MARROW

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2ZEE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:159 -Gly A:160
2His A:228 -Pro A:229
3Ser A:323 -Pro A:324
4Asp B:159 -Gly B:160
5His B:228 -Pro B:229
6Ser B:323 -Pro B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053956R54WQPCT_HUMANPolymorphism2255991A/BR54W
2UniProtVAR_005569Q71RQPCT_HUMANPolymorphism  ---A/BQ71R
3UniProtVAR_053957H360PQPCT_HUMANPolymorphism4670696A/BH360P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053956R54WQPCT_HUMANPolymorphism2255991AR54W
2UniProtVAR_005569Q71RQPCT_HUMANPolymorphism  ---AQ71R
3UniProtVAR_053957H360PQPCT_HUMANPolymorphism4670696AH360P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053956R54WQPCT_HUMANPolymorphism2255991BR54W
2UniProtVAR_005569Q71RQPCT_HUMANPolymorphism  ---BQ71R
3UniProtVAR_053957H360PQPCT_HUMANPolymorphism4670696BH360P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (3, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053956R54WQPCT_HUMANPolymorphism2255991A/BR54W
2UniProtVAR_005569Q71RQPCT_HUMANPolymorphism  ---A/BQ71R
3UniProtVAR_053957H360PQPCT_HUMANPolymorphism4670696A/BH360P

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003384151aENSE00001279566chr2:37571717-37571994278QPCT_HUMAN1-40402A:33-40
B:33-40
8
8
1.2ENST000003384152ENSE00001279532chr2:37579932-37580078147QPCT_HUMAN41-89492A:41-89
B:41-89
49
49
1.4aENST000003384154aENSE00001279523chr2:37586723-37587001279QPCT_HUMAN90-182932A:90-182
B:90-182
93
93
1.5bENST000003384155bENSE00000747404chr2:37594375-37594551177QPCT_HUMAN183-241592A:189-241
B:189-241
53
53
1.7bENST000003384157bENSE00000747405chr2:37596828-37596927100QPCT_HUMAN242-275342A:242-275
B:242-275
34
34
1.8ENST000003384158ENSE00001279502chr2:37599499-37599615117QPCT_HUMAN275-314402A:275-314
B:275-314
40
40
1.9dENST000003384159dENSE00001379586chr2:37599825-37600465641QPCT_HUMAN314-361482A:314-361
B:314-361
48
48

(-) 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:323
 aligned with QPCT_HUMAN | Q16769 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:329
                                    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         
           QPCT_HUMAN    33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
               SCOP domains d2zeea_ A: Glutaminyl-peptide cyclotransferase, QPCT                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeeeeeeee......eeeeeeeee......eeeeeeee...................hhhhhhhhhhhhhhhhhhhhh..------..eeeeeeee..............hhhhhhhhhhhhh..........hhhhheeeeeee.............hhhhhhhhhhhhhhhhhhhhh.........................hhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------W----------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a    Exon 1.2  PDB: A:41-89 UniProt: 41-89            Exon 1.4a  PDB: A:90-182 UniProt: 90-182                                                     Exon 1.5b  PDB: A:189-241 UniProt: 183-241 [INCOMPLETE]    Exon 1.7b  PDB: A:242-275         --------------------------------------Exon 1.9d  PDB: A:314-361 UniProt: 314-361       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:275-314                ----------------------------------------------- Transcript 1 (2)
                 2zee A  33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDGAVPCAMMLELARALDKKLLSLK------PDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
                                    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         
                                                                                                                                                                               182    189                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with QPCT_HUMAN | Q16769 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:329
                                    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         
           QPCT_HUMAN    33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
               SCOP domains d2zeeb_ B: Glutaminyl-peptide cyclotransferase, QPCT                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------Peptidase_M28-2zeeB01 B:133-345                                                                                                                                                                                      ---------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------Peptidase_M28-2zeeB02 B:133-345                                                                                                                                                                                      ---------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeee......eeeeeeee.......hhhhh.......hhhhhhhhhhhhhhhhhhhhh..------..eeeeeeee..............hhhhhhhhhhhhh..........hhhh.eeeeeee.........eee.hhhhhhhhhhhhhhhhhhhhh......hhhhh.eeeee........hhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------W----------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a    Exon 1.2  PDB: B:41-89 UniProt: 41-89            Exon 1.4a  PDB: B:90-182 UniProt: 90-182                                                     Exon 1.5b  PDB: B:189-241 UniProt: 183-241 [INCOMPLETE]    Exon 1.7b  PDB: B:242-275         --------------------------------------Exon 1.9d  PDB: B:314-361 UniProt: 314-361       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:275-314                ----------------------------------------------- Transcript 1 (2)
                 2zee B  33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDGAVPCAMMLELARALDKKLLSLK------PDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
                                    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         
                                                                                                                                                                               182    189                                                                                                                                                                            

   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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (QPCT_HUMAN | Q16769)
molecular function
    GO:0016603    glutaminyl-peptide cyclotransferase activity    Catalysis of the reaction: L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0017186    peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase    The chemical reactions and pathways resulting in the formation of peptidyl-pyroglutamic acid, catalyzed by glutaminyl-peptide cyclotransferase.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  Cis Peptide Bonds
    Asp A:159 - Gly A:160   [ RasMol ]  
    Asp B:159 - Gly B:160   [ RasMol ]  
    His A:228 - Pro A:229   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        QPCT_HUMAN | Q167691moi 2afm 2afo 2afs 2afu 2afw 2afx 2afz 2zed 2zef 2zeg 2zeh 2zel 2zem 2zen 2zeo 2zep 3pbb 3pbe 3si0 4yu9 4ywy

(-) Related Entries Specified in the PDB File

2afm THE WILD-TYPE HUMAN GLUTAMINYL CYCLASE
2zed
2zef
2zeg
2zeh
2zel
2zem
2zen
2zeo
2zep