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Biol. Unit 1 - sites (Jmol Viewer)

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

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

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

Summary Information (see also Sequences/Alignments below)

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

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

(no "SS Bond" information available for 3CTZ)

Asymmetric Unit

No.	Residues
1	Gly A:500	-	Pro A:501

(no "SAP(SNP)/Variant" information available for 3CTZ)

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

(no "Exon" information available for 3CTZ)

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

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 '\|'

(no "SCOP Domain" information available for 3CTZ)

(no "CATH Domain" information available for 3CTZ)

(no "Pfam Domain" information available for 3CTZ)

Asymmetric Unit(hide GO term definitions)

Chain A (XPP1_HUMAN | Q9NQW7)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0070006	metalloaminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0010815	bradykinin catabolic process	The chemical reactions and pathways resulting in the breakdown of the peptide bradykinin.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P6G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:500 - Pro A:501	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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