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Title :   HUMAN CARBOXYPEPTIDASE A4 IN COMPLEX WITH A CLEAVED HEXAPEPTIDE.

Authors :   A. Bayes, D. Fernandez, M. Sola, A. Marrero, S. Garcia-Pique, F. X. Avil J. Vendrell, F. X. Gomis-Ruth

Date :   30 Mar 07 (Deposition) - 17 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Metallocarboxypeptidase; Metalloprotease; Product; Cleavage; Specificity; Human Carboxypeptidase A4, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Bayes, D. Fernandez, M. Sola, A. Marrero, S. Garcia-Pique, F. X. Aviles, J. Vendrell, F. X. Gomis-Ruth
Caught After The Act: A Human A-Type Metallocarboxypeptidas In A Product Complex With A Cleaved Hexapeptide.
Biochemistry V. 46 6921 2007
PubMed-ID: 17506531 | Reference-DOI: 10.1021/BI700480B

Molecule 1 - CARBOXYPEPTIDASE A4
	Chains	:	A
	EC Number	:	3.4.17.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PPIC9
	Fragment	:	CARBOXYPEPTIDASE A4
	Gene	:	CPA4, CPA3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBOXYPEPTIDASE A3

Molecule 2 - PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESISED
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SCN	1	Ligand/Ion	THIOCYANATE ION
5	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:148 , HOH A:679	BINDING SITE FOR RESIDUE NAG A 901
2	AC2	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , VAL B:5	BINDING SITE FOR RESIDUE ZN A 999
3	AC3	SOFTWARE	LYS A:37 , THR A:54 , THR A:97 , GLU A:101 , HOH A:584 , HOH A:766	BINDING SITE FOR RESIDUE SCN A 502
4	AC4	SOFTWARE	HIS A:69 , ARG A:127 , ASN A:144 , ARG A:145 , HIS A:196 , MET A:203 , THR A:243 , VAL A:247 , TYR A:248 , THR A:268 , GLU A:270 , VAL B:5 , HOH B:556 , HOH B:605	BINDING SITE FOR RESIDUE ASP B 6
5	AC5	SOFTWARE	TRP A:73 , ARG A:124 , LEU A:280 , LEU A:281 , HOH A:548	BINDING SITE FOR RESIDUE GOL A 501

Asymmetric/Biological Unit

No.	Residues
1	A:138	-	A:161

Asymmetric/Biological Unit

No.	Residues
1	Ser A:197	-	Tyr A:198
2	Pro A:205	-	Tyr A:206
3	Arg A:272	-	Asp A:273

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020393	P	157	T	CBPA4_HUMAN	Polymorphism	3735051	A	P	46	T
2	UniProt	VAR_048595	R	183	L	CBPA4_HUMAN	Polymorphism	3735053	A	R	71	L
3	UniProt	VAR_020394	G	303	C	CBPA4_HUMAN	Polymorphism	2171492	A	G	191	C

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPA4_HUMAN	172-194	1	A:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPA4_HUMAN	308-318	1	A:196-206

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000222482	1a	ENSE00001175329	chr7:129932993-129933088	96	CBPA4_HUMAN	1-23	23	0	-	-
1.3	ENST00000222482	3	ENSE00000882290	chr7:129938586-129938667	82	CBPA4_HUMAN	23-50	28	0	-	-
1.4a	ENST00000222482	4a	ENSE00000723226	chr7:129939110-129939244	135	CBPA4_HUMAN	51-95	45	0	-	-
1.6	ENST00000222482	6	ENSE00000723228	chr7:129940656-129940754	99	CBPA4_HUMAN	96-128	33	1	A:5-17	13
1.7c	ENST00000222482	7c	ENSE00000723230	chr7:129944318-129944419	102	CBPA4_HUMAN	129-162	34	1	A:18-51	34
1.8b	ENST00000222482	8b	ENSE00000723233	chr7:129945656-129945760	105	CBPA4_HUMAN	163-197	35	1	A:52-85	35
1.9c	ENST00000222482	9c	ENSE00000723234	chr7:129946627-129946737	111	CBPA4_HUMAN	198-234	37	1	A:86-122	37
1.10b	ENST00000222482	10b	ENSE00000723236	chr7:129948147-129948237	91	CBPA4_HUMAN	235-265	31	1	A:123-153	31
1.11	ENST00000222482	11	ENSE00000723239	chr7:129950627-129950826	200	CBPA4_HUMAN	265-331	67	1	A:153-219	67
1.12	ENST00000222482	12	ENSE00000723240	chr7:129951878-129951962	85	CBPA4_HUMAN	332-360	29	1	A:220-248	29
1.13b	ENST00000222482	13b	ENSE00001279439	chr7:129962329-129964019	1691	CBPA4_HUMAN	360-421	62	1	A:248-308	61

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
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Chain A from PDB  Type:PROTEIN  Length:305
 aligned with CBPA4_HUMAN | Q9UI42 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:305
                                   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     
          CBPA4_HUMAN   116 NNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 420
               SCOP domains d2pcua1 A:5-307 Carboxypeptidase A                                                                                                                                                                                                                                                                              - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Peptidase_M14-2pcuA01 A:18-296                                                                                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee.........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------T-------------------------L-----------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6     Exon 1.7c  PDB: A:18-51           Exon 1.8b  PDB: A:52-85            Exon 1.9c  PDB: A:86-122             Exon 1.10b  PDB: A:123-153     ------------------------------------------------------------------Exon 1.12  PDB: A:220-248    ------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:153-219 UniProt: 265-331                         ----------------------------Exon 1.13b  PDB: A:248-308 UniProt: 360-421 [INCOMPLETE]      Transcript 1 (2)
                 2pcu A   5 NNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 308
                                    14        24        34        44        54 |      63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
                                                                             55A

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 2pcu B   1 FNRPV   5

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/Biological 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: Pancreatic carboxypeptidases (77)

Protein domain: Carboxypeptidase A (41)

Human (Homo sapiens) [TaxId: 9606] (5)

d2pcua1

A:5-307

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MH (119)

Family: Peptidase_M14 (33)

Homo sapiens (Human) (5)

Peptidase_M14-2pcuA01

A:18-296

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBPA4_HUMAN | Q9UI42)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:272 - Asp A:273	[ RasMol ]
		Pro A:205 - Tyr A:206	[ RasMol ]
		Ser A:197 - Tyr A:198	[ RasMol ]

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	2pcu
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	3.4.17.-
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	CBPA4_HUMAN \| Q9UI42	:	2bo9 2boa 4a94 4bd9

2bo9	COMPLEX OF THE SAME PROTEASE WITH A PROTEIN INHIBITOR, LATEXIN.
2boa	STRUCTURE OF THE PROENZYME.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (3, 3)

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Exons (8, 8)

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