2AFO - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GLUTAMINYL CYCLASE AT PH 8.0

Authors :   K. F. Huang, Y. L. Liu, W. J. Cheng, T. P. Ko, A. H. J. Wang

Date :   26 Jul 05 (Deposition) - 23 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (3x)

Keywords :   Alpha-Beta Protein, Metalloprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. F. Huang, Y. L. Liu, W. J. Cheng, T. P. Ko, A. H. Wang
Crystal Structures Of Human Glutaminyl Cyclase, An Enzyme Responsible For Protein N-Terminal Pyroglutamate Formation
Proc. Natl. Acad. Sci. Usa V. 102 13117 2005
PubMed-ID: 16135565 | Reference-DOI: 10.1073/PNAS.0504184102

Molecule 1 - GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.3.2.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 33-361
	Gene	:	QPCT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	QC, GLUTAMINYL-TRNA CYCLOTRANSFERASE, GLUTAMINYL CYCLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:159 , GLU A:202 , HIS A:330 , HOH A:401	BINDING SITE FOR RESIDUE ZN A 391
2	AC2	SOFTWARE	LYS A:144 , LEU A:205 , HIS A:206 , TRP A:207 , ASN A:263 , TRP A:329 , HIS A:330 , HOH A:576 , HOH A:704	BINDING SITE FOR RESIDUE SO4 A 395
3	AC3	SOFTWARE	ASP B:159 , GLU B:202 , HIS B:330 , HOH B:402	BINDING SITE FOR RESIDUE ZN B 392
4	AC4	SOFTWARE	LYS B:40 , LYS B:144 , HIS B:206 , TRP B:207 , HOH B:608 , HOH B:733	BINDING SITE FOR RESIDUE SO4 B 396

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

Asymmetric Unit

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

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053956	R	54	W	QPCT_HUMAN	Polymorphism	2255991	A/B	R	54	W
2	UniProt	VAR_005569	Q	71	R	QPCT_HUMAN	Polymorphism	---	A/B	Q	71	R
3	UniProt	VAR_053957	H	360	P	QPCT_HUMAN	Polymorphism	4670696	A/B	H	360	P

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053956	R	54	W	QPCT_HUMAN	Polymorphism	2255991	A	R	54	W
2	UniProt	VAR_005569	Q	71	R	QPCT_HUMAN	Polymorphism	---	A	Q	71	R
3	UniProt	VAR_053957	H	360	P	QPCT_HUMAN	Polymorphism	4670696	A	H	360	P

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053956	R	54	W	QPCT_HUMAN	Polymorphism	2255991	B	R	54	W
2	UniProt	VAR_005569	Q	71	R	QPCT_HUMAN	Polymorphism	---	B	Q	71	R
3	UniProt	VAR_053957	H	360	P	QPCT_HUMAN	Polymorphism	4670696	B	H	360	P

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

Biological Unit 3 (3, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053956	R	54	W	QPCT_HUMAN	Polymorphism	2255991	A/B	R	54	W
2	UniProt	VAR_005569	Q	71	R	QPCT_HUMAN	Polymorphism	---	A/B	Q	71	R
3	UniProt	VAR_053957	H	360	P	QPCT_HUMAN	Polymorphism	4670696	A/B	H	360	P

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

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

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000338415	1a	ENSE00001279566	chr2:37571717-37571994	278	QPCT_HUMAN	1-40	40	2	A:33-40 B:33-40	8 8
1.2	ENST00000338415	2	ENSE00001279532	chr2:37579932-37580078	147	QPCT_HUMAN	41-89	49	2	A:41-89 B:41-89	49 49
1.4a	ENST00000338415	4a	ENSE00001279523	chr2:37586723-37587001	279	QPCT_HUMAN	90-182	93	2	A:90-181 B:90-181	92 92
1.5b	ENST00000338415	5b	ENSE00000747404	chr2:37594375-37594551	177	QPCT_HUMAN	183-241	59	2	A:190-241 B:190-241	52 52
1.7b	ENST00000338415	7b	ENSE00000747405	chr2:37596828-37596927	100	QPCT_HUMAN	242-275	34	2	A:242-275 B:242-275	34 34
1.8	ENST00000338415	8	ENSE00001279502	chr2:37599499-37599615	117	QPCT_HUMAN	275-314	40	2	A:275-314 B:275-314	40 40
1.9d	ENST00000338415	9d	ENSE00001379586	chr2:37599825-37600465	641	QPCT_HUMAN	314-361	48	2	A:314-361 B:314-361	48 48

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:321
 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 d2afoa_ A: Glutaminyl-peptide cyclotransferase, QPCT                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....eeeeeeeeee......eeeeeeeeee.....eeeeeeee...................hhhhhhhhhhhhhhhhhhhh..--------.eeeeeeee..............hhhhhhhhhhhhh...............eeeeeee.............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:90-181 UniProt: 90-182 [INCOMPLETE]                                        Exon 1.5b  PDB: A:190-241 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)
                 2afo A  33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSL--------DLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172        |-       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352         
                                                                                                                                                                              181      190

Chain B from PDB  Type:PROTEIN  Length:321
 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 d2afob_ B: Glutaminyl-peptide cyclotransferase, QPCT                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeee.......hhhhh.......hhhhhhhhhhhhhhhhhhhh..--------.eeeeeeee..............hhhhhhhhhhhhh..........hhhh.eeeeeee.............hhhhhhhhhhhhhhhhhhhhh......hhhhh..............hhhhhh....eeee...................hhhhhhhhhhhhhhhhhhhhh. 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:90-181 UniProt: 90-182 [INCOMPLETE]                                        Exon 1.5b  PDB: B:190-241 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)
                 2afo B  33 ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSL--------DLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL 361
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172        |-       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352         
                                                                                                                                                                              181      190

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Zn-dependent exopeptidases (214)

Family: Glutaminyl-peptide cyclotransferase-like (22)

Protein domain: Glutaminyl-peptide cyclotransferase, QPCT (22)

Human (Homo sapiens) [TaxId: 9606] (20)

1a	d2afoa_	A:
1b	d2afob_	B:

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

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

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:159 - Ser A:160	[ RasMol ]
		Asp B:159 - Ser B:160	[ RasMol ]
		His A:228 - Pro A:229	[ RasMol ]
		His B:228 - Pro B:229	[ RasMol ]
		Ser A:323 - Pro A:324	[ RasMol ]
		Ser B:323 - Pro B:324	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	2afo
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Access by UniProt ID/Accession number
	QPCT_HUMAN \| Q16769
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	2.3.2.5
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2afs	THE GENETIC MUTANT R54W OF HUMAN GLUTAMINYL CYCLASE
2afu	HUMAN GLUTAMINYL CYCLASE IN COMPLEX WITH GLUTAMINE T-BUTYL ESTER
2afw	HUMAN GLUTAMINYL CYCLASE IN COMPLEX WITH N-ACETYLHISTAMINE
2afx	HUMAN GLUTAMINYL CYCLASE, AN ENZYME RESPONSIBLE
2afz	HUMAN GLUTAMINYL CYCLASE IN COMPLEX WITH 1-VINYLIMIDAZOLE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (0, 0)

Exons (7, 14)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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