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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PROLIDASE

Authors :   U. Mueller, F. H. Niesen, Y. Roske, F. Goetz, J. Behlke, K. Buessow, U. H

Date :   24 Jun 06 (Deposition) - 05 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

Chains :   Asym./Biol. Unit : A,B

Keywords :   Metallocarboxypeptidase, Disease Mutation, Xaa-Pro Dipeptidase, Dipeptidase, Peptidase D, Collagen Degradation, Metalloaminopeptidase, Enzyme, Protease, Pepd Gene, Manganese, Hydrolase, Metal- Binding, Metalloprotease, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Mueller, F. H. Niesen, Y. Roske, F. Goetz, J. Behlke, K. Buessow, U. Heinemann
Crystal Structure Of Human Prolidase: The Molecular Basis Of Pd Disease
To Be Published
PubMed: search

Molecule 1 - XAA-PRO DIPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.13.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	RZPD CLONE ID PSFEP250H122
	Expression System Strain	:	SCS1/PRARE
	Expression System Taxid	:	562
	Expression System Vector	:	PQTEV
	Organ	:	FOETAL BRAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	RZPD GERMAN RESOURCE CENTER CDNA CLONE MPMGP800M05547
	Synonym	:	PROLIDASE, X-PRO DIPEPTIDASE, PROLINE DIPEPTIDASE, IMIDODIPEPTIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	NA	5	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:288 , HIS A:371 , GLU A:413 , GLU A:453 , NA A:1485 , HOH A:2404	BINDING SITE FOR RESIDUE NA A1484
2	AC2	SOFTWARE	ASP A:277 , ASP A:288 , GLU A:453 , NA A:1484	BINDING SITE FOR RESIDUE NA A1485
3	AC3	SOFTWARE	GLY A:319 , HOH A:2362 , HOH A:2470 , ALA B:40	BINDING SITE FOR RESIDUE NA A1486
4	AC4	SOFTWARE	ASP B:277 , ASP B:288 , GLU B:453 , NA B:1485 , HOH B:2361	BINDING SITE FOR RESIDUE NA B1484
5	AC5	SOFTWARE	ASP B:288 , HIS B:371 , GLU B:413 , GLU B:453 , NA B:1484 , HOH B:2417	BINDING SITE FOR RESIDUE NA B1485

(no "SS Bond" information available for 2IW2)

(no "Cis Peptide Bond" information available for 2IW2)

Asymmetric/Biological Unit (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011614	R	184	Q	PEPD_HUMAN	Disease (PD)	121917722	A/B	R	185	Q
2	UniProt	VAR_004404	D	276	N	PEPD_HUMAN	Disease (PD)	121917721	A/B	D	277	N
3	UniProt	VAR_011615	G	278	D	PEPD_HUMAN	Disease (PD)	121917723	A/B	G	279	D
4	UniProt	VAR_051574	R	388	H	PEPD_HUMAN	Polymorphism	2230062	A/B	R	389	H
5	UniProt	VAR_014723	L	435	F	PEPD_HUMAN	Polymorphism	17570	A/B	F	436	F
6	UniProt	VAR_004405	G	448	R	PEPD_HUMAN	Disease (PD)	121917724	A/B	G	449	R

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROLINE_PEPTIDASE	PS00491	Aminopeptidase P and proline dipeptidase signature.	PEPD_HUMAN	366-378	2	A:367-379 B:367-379

Asymmetric/Biological Unit (15, 30)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000244137	1	ENSE00001356571	chr19:34012801-34012650	152	PEPD_HUMAN	1-6	6	2	A:7-7 B:7-7	1 1
1.2	ENST00000244137	2	ENSE00000896667	chr19:34003682-34003499	184	PEPD_HUMAN	6-67	62	2	A:7-68 B:7-68	62 62
1.3	ENST00000244137	3	ENSE00000896666	chr19:34002061-34001934	128	PEPD_HUMAN	68-110	43	2	A:69-111 B:69-111	43 43
1.4	ENST00000244137	4	ENSE00000953262	chr19:33991907-33991844	64	PEPD_HUMAN	110-131	22	2	A:111-132 B:111-132	22 22
1.5	ENST00000244137	5	ENSE00001012845	chr19:33984243-33984196	48	PEPD_HUMAN	132-147	16	2	A:133-148 B:133-148	16 16
1.6	ENST00000244137	6	ENSE00000953263	chr19:33980963-33980902	62	PEPD_HUMAN	148-168	21	2	A:149-169 B:149-169	21 21
1.7	ENST00000244137	7	ENSE00000896664	chr19:33968996-33968952	45	PEPD_HUMAN	168-183	16	2	A:169-184 B:169-184	16 16
1.8	ENST00000244137	8	ENSE00000695478	chr19:33954968-33954893	76	PEPD_HUMAN	183-208	26	2	A:184-209 B:184-209	26 26
1.9	ENST00000244137	9	ENSE00000695480	chr19:33953947-33953901	47	PEPD_HUMAN	209-224	16	2	A:210-225 B:210-225	16 16
1.10	ENST00000244137	10	ENSE00000896661	chr19:33904549-33904481	69	PEPD_HUMAN	224-247	24	2	A:225-248 B:225-248	24 24
1.11	ENST00000244137	11	ENSE00000896659	chr19:33902655-33902578	78	PEPD_HUMAN	247-273	27	2	A:248-274 B:248-274	27 27
1.12	ENST00000244137	12	ENSE00000896656	chr19:33892775-33892627	149	PEPD_HUMAN	273-323	51	2	A:274-324 B:274-324	51 51
1.13	ENST00000244137	13	ENSE00000695490	chr19:33882385-33882201	185	PEPD_HUMAN	323-384	62	2	A:324-385 B:324-385	62 62
1.14	ENST00000244137	14	ENSE00001261724	chr19:33878987-33878796	192	PEPD_HUMAN	385-448	64	2	A:386-449 B:386-449	64 64
1.15	ENST00000244137	15	ENSE00000846271	chr19:33878387-33877865	523	PEPD_HUMAN	449-493	45	2	A:450-484 B:450-484	35 35

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:478
 aligned with PEPD_HUMAN | P12955 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:478
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475        
           PEPD_HUMAN     6 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCD 483
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhh.......eeeee..................hhhhhhhhh......eeeee.....eeeee...hhhhh.......hhhhhhhhhh..eeee..hhhhhhhhh.........................hhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........eeeeehhhhh..................eeeeee..........eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh............................hhhhh........eeeeee..eeeehhhhhhhhhhhhhhhh...hhhhhhhh..eeeee.eeeee....eeee.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------N-D-------------------------------------------------------------------------------------------------------------H----------------------------------------------F------------R----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI--------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-------------------------------------------------------------Exon 1.3  PDB: A:69-111 UniProt: 68-110    ---------------------Exon 1.5        Exon 1.6             --------------Exon 1.8  PDB: A:184-209  ---------------Exon 1.10  PDB: A:225-24-------------------------Exon 1.12  PDB: A:274-324 UniProt: 273-323         -------------------------------------------------------------Exon 1.14  PDB: A:386-449 UniProt: 385-448                      Exon 1.15  PDB: A:450-484           Transcript 1 (1)
           Transcript 1 (2) Exon 1.2  PDB: A:7-68 UniProt: 6-67                           ------------------------------------------Exon 1.4              ------------------------------------Exon 1.7        -------------------------Exon 1.9        ----------------------Exon 1.11  PDB: A:248-274  -------------------------------------------------Exon 1.13  PDB: A:324-385 UniProt: 323-384                    --------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2iw2 A   7 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFFNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCD 484
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476

Chain B from PDB  Type:PROTEIN  Length:478
 aligned with PEPD_HUMAN | P12955 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:478
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475        
           PEPD_HUMAN     6 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCD 483
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhh.......eeeee..................hhhhhhhhh......eeeee.....eeeee...hhhhh.......hhhhhhhhhh..eeee..hhhhhhhhh.........................hhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........eeee.hhhhh..................eeeeee..........eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh............................hhhhh..........eeee..eeeehhhhhhhhhhhhhhhh...hhhhh.....eeeee.eeeee....eeee.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------N-D-------------------------------------------------------------------------------------------------------------H----------------------------------------------F------------R----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI--------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-------------------------------------------------------------Exon 1.3  PDB: B:69-111 UniProt: 68-110    ---------------------Exon 1.5        Exon 1.6             --------------Exon 1.8  PDB: B:184-209  ---------------Exon 1.10  PDB: B:225-24-------------------------Exon 1.12  PDB: B:274-324 UniProt: 273-323         -------------------------------------------------------------Exon 1.14  PDB: B:386-449 UniProt: 385-448                      Exon 1.15  PDB: B:450-484           Transcript 1 (1)
           Transcript 1 (2) Exon 1.2  PDB: B:7-68 UniProt: 6-67                           ------------------------------------------Exon 1.4              ------------------------------------Exon 1.7        -------------------------Exon 1.9        ----------------------Exon 1.11  PDB: B:248-274  -------------------------------------------------Exon 1.13  PDB: B:324-385 UniProt: 323-384                    --------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2iw2 B   7 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFFNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCD 484
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476

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 2IW2)

(no "CATH Domain" information available for 2IW2)

(no "Pfam Domain" information available for 2IW2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PEPD_HUMAN | P12955)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	GO:0016805	dipeptidase activity	Catalysis of the hydrolysis of a dipeptide.
	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:0004181	metallocarboxypeptidase activity	Catalysis of the hydrolysis of C-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:0102009	proline dipeptidase activity	Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal <=> L-proline + a standard alpha amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Asymmetric/Biological Unit
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	2iw2
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	3.4.13.9
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	PEPD_HUMAN \| P12955	:	2okn 5m4g 5m4j 5m4l 5m4q

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 12)

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Exons (15, 30)

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