3CTZ - JenaLib

Title :   STRUCTURE OF HUMAN CYTOSOLIC X-PROLYL AMINOPEPTIDASE

Authors :   X. Li, Z. Lou, Z. Rao

Date :   15 Apr 08 (Deposition) - 27 May 08 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Pita-Bread Fold, Aminopeptidase, Hydrolase, Manganese, Metal-Binding, Metalloprotease, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Li, Z. Lou, X. Li, W. Zhou, M. Ma, Y. Cao, Y. Geng, M. Bartlam, X. C. Zhang, Z. Rao
Structure Of Human Cytosolic X-Prolyl Aminopeptidase: A Double Mn(Ii)-Dependent Dimeric Enzyme With A Novel Three-Domain Subunit
J. Biol. Chem. V. 283 22858 2008
PubMed-ID: 18515364 | Reference-DOI: 10.1074/JBC.M710274200

Compounds

Molecule 1 - XAA-PRO AMINOPEPTIDASE 1
	Chains	:	A
	EC Number	:	3.4.11.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	XPNPEP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	X-PRO AMINOPEPTIDASE 1, X-PROLYL AMINOPEPTIDASE 1, SOLUBLE, CYTOSOLIC AMINOPEPTIDASE P, SOLUBLE AMINOPEPTIDASE P, SAMP, AMINOACYLPROLINE AMINOPEPTIDASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 5)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	NA	1	Ligand/Ion	SODIUM ION
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:426 , HIS A:489 , GLU A:523 , GLU A:537 , HOH A:644 , HOH A:1519 , HOH A:1520	BINDING SITE FOR RESIDUE MN A 624
2	AC2	SOFTWARE	PHE A:381 , ASP A:415 , ASP A:426 , THR A:428 , GLU A:537 , HOH A:644 , HOH A:1518	BINDING SITE FOR RESIDUE MN A 625
3	AC3	SOFTWARE	ASP A:281 , THR A:435 , HOH A:658 , HOH A:670 , HOH A:717 , HOH A:739 , HOH A:752	BINDING SITE FOR RESIDUE CA A 626
4	AC4	SOFTWARE	GLY A:486 , LYS A:507	BINDING SITE FOR RESIDUE NA A 627
5	AC5	SOFTWARE	PHE A:381 , ILE A:394 , HIS A:395 , HIS A:485 , GLY A:486 , HIS A:489 , HIS A:498 , GLU A:523 , HOH A:659 , HOH A:792 , HOH A:861 , HOH A:1298 , HOH A:1518 , HOH A:1520	BINDING SITE FOR RESIDUE P6G A 628

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	XPP1_HUMAN	485-497	1	A:485-497

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	XPP1_HUMAN	485-497	2	A:485-497

Exons (0, 0)

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:617
 aligned with XPP1_HUMAN | Q9NQW7 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:617
                                    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       492       502       512       522       532       542       552       562       572       582       592       602       612       
           XPP1_HUMAN     3 PKVTSELLRQLRQAMRNSEYVTEPIQAYIIPSGDAHQSEYIAPCDCRRAFVSGFDGSAGTAIITEEHAAMWTDGRYFLQAAKQMDSNWTLMKMGLKDTPTQEDWLVSVLPEGSRVGVDPLIIPTDYWKKMAKVLRSAGHHLIPVKENLVDKIWTDRPERPCKPLLTLGLDYTGISWKDKVADLRLKMAERNVMWFVVTALDEIAWLFNLRGSDVEHNPVFFSYAIIGLETIMLFIDGDRIDAPSVKEHLLLDLGLEAEYRIQVHPYKSILSELKALCADLSPREKVWVSDKASYAVSETIPKDHRCCMPYTPICIAKAVKNSAESEGMRRAHIKDAVALCELFNWLEKEVPKGGVTEISAADKAEEFRRQQADFVDLSFPTISSTGPNGAIIHYAPVPETNRTLSLDEVYLIDSGAQYKDGTTDVTRTMHFGTPTAYEKECFTYVLKGHIAVSAAVFPTGTKGHLLDSFARSALWDSGLDYLHGTGHGVGSFLNVHEGPCGISYKTFSDEPLEAGMIVTDEPGYYEDGAFGIRIENVVLVVPVKTKYNFNNRGSLTFEPLTLVPIQTKMIDVDSLTDKECDWLNNYHLTCRDVIGKELQKQGRQEALEWLIRETQPI 619
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...........eeee...........hhhhhhhhhhhh......eeeee...eeeeehhhhhhhhhhhh...eeeee.......hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh..eeee...hhhhhhh...........ee.hhhhhh.hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhee............eeeee...eeee..hhhhhhhhhhhhh......hhhh.eeeehhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh.eeee..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeee....eeee.hhhhh.....hhhhh........eeeee.eee..ee..eeeee.....hhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhh........ee.............ee..............eeee..eeee...eeee..eeeeeeee..........eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI-------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ctz A   3 PKVTSELLRQLRQAMRNSEYVTEPIQAYIIPSGDAHQSEYIAPCDCRRAFVSGFDGSAGTAIITEEHAAMWTDGRYFLQAAKQMDSNWTLMKMGLKDTPTQEDWLVSVLPEGSRVGVDPLIIPTDYWKKMAKVLRSAGHHLIPVKENLVDKIWTDRPERPCKPLLTLGLDYTGISWKDKVADLRLKMAERNVMWFVVTALDEIAWLFNLRGSDVEHNPVFFSYAIIGLETIMLFIDGDRIDAPSVKEHLLLDLGLEAEYRIQVHPYKSILSELKALCADLSPREKVWVSDKASYAVSETIPKDHRCCMPYTPICIAKAVKNSAESEGMRRAHIKDAVALCELFNWLEKEVPKGGVTEISAADKAEEFRRQQADFVDLSFPTISSTGPTGAIIHYAPVPETNRTLSLDEVYLIDSGAQYKDGTTDVTRTMHFETPTAYEKECFTYVLKGHIAVSAAVFPTGTKGHLLDSFARSALWDSGLDYLHGTGHGVGSFLNVHEGPCGISYKTFSDEPLEAGMIVTDEPGYYEDGAFGIRIENVVLVVPVKTKYNFNNRGSLTLEPLTLVPIQTKMIDVDSLTDKECDWLNNYHLTCRDVIGKELQKQGRQEALEWLIRETQPI 619
                                    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       492       502       512       522       532       542       552       562       572       582       592       602       612

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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