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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF THE COMPLEX BETWEEN SMCI AND HUMAN CARBOXYPEPTIDASE A4

Authors :   M. Alonso-Del-Ribero, M. L. Reytor, S. A. Trejo, M. A. Chavez, F. X. Avil D. Reverter

Date :   05 Oct 12 (Deposition) - 17 Jul 13 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Hydrolase-Hydrolase Inhibitor Complex, Serine Protease Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Alonso Del Rivero, M. L. Reytor, S. A. Trejo, M. A. Chavez, F. X. Aviles, D. Reverter
A Noncanonical Mechanism Of Carboxypeptidase Inhibition Revealed By The Crystal Structure Of The Tri-Kunitz Smci In Complex With Human Cpa4.
Structure V. 21 1118 2013
PubMed-ID: 23746805 | Reference-DOI: 10.1016/J.STR.2013.04.021

Molecule 1 - CARBOXYPEPTIDASE A4
	Chains	:	A
	EC Number	:	3.4.17.-
	Engineered	:	YES
	Expression System	:	KOMAGATAELLA PASTORIS
	Expression System Plasmid	:	PPICZAA
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 112-421
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBOXYPEPTIDASE A3

Molecule 2 - CARBOXYPEPTIDASE INHIBITOR SMCI
	Chains	:	B
	Engineered	:	YES
	Expression System	:	KOMAGATAELLA PASTORIS
	Expression System Plasmid	:	PPICZAA
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	SABELLASTARTE MAGNIFICA
	Organism Taxid	:	389514
	Synonym	:	SMCI INHIBITOR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , HOH A:2032 , ILE B:1	BINDING SITE FOR RESIDUE ZN A 500

Asymmetric/Biological Unit

No.	Residues
1	A:138	-	A:161
2	B:4	-	B:54
3	B:13	-	B:37
4	B:29	-	B:50
5	B:56	-	B:106
6	B:65	-	B:89
7	B:81	-	B:102
8	B:115	-	B:165
9	B:124	-	B:148
10	B:140	-	B: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	45	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 (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPTI_KUNITZ_2	PS50279	Pancreatic trypsin inhibitor (Kunitz) family profile.	PCPI_SABMA	4-54 56-106 115-165	3	B:4-54 B:56-106 B:115-165
2	BPTI_KUNITZ_1	PS00280	Pancreatic trypsin inhibitor (Kunitz) family signature.	PCPI_SABMA	32-50 84-102 143-161	3	B:32-50 B:84-102 B:143-161
3	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPA4_HUMAN	172-194	1	A:60-82
4	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:5-16	12
1.7c	ENST00000222482	7c	ENSE00000723230	chr7:129944318-129944419	102	CBPA4_HUMAN	129-162	34	1	A:17-50	34
1.8b	ENST00000222482	8b	ENSE00000723233	chr7:129945656-129945760	105	CBPA4_HUMAN	163-197	35	1	A:51-85	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
	(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:304
 aligned with CBPA4_HUMAN | Q9UI42 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:304
                                   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    
          CBPA4_HUMAN   117 NFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 420
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee.........eeeeee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. 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:17-50           Exon 1.8b  PDB: A:51-85            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)
                 4bd9 A   5 NFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with PCPI_SABMA | P84875 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           PCPI_SABMA     1 ISVCDLPADRGQCTAYIPQWFFNKTTEDCEKFVYGGCQGNANRFETKDDCIANCGCNLPSKVGPCRVSARMWFHNPETEKCEVFIYGGCHGNANRFATETECQEVCDRYQKPGFCYQPSETGPCKGSFPRYYYDYEDGECKEFIYGGCEGNANNFETKESCENAC 165
               SCOP domains d4bd9b1 B:1-54 automated matches                      d4bd9b2 B:55-109 automated matches                     d4bd9b3 B:110-165 automated matches                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh.............eeeeeee....eeeeeee...........hhhhhhhhhh....hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---BPTI_KUNITZ_2  PDB: B:4-54 UniProt: 4-54           -BPTI_KUNITZ_2  PDB: B:56-106 UniProt: 56-106       --------BPTI_KUNITZ_2  PDB: B:115-165 UniProt: 115-165      PROSITE (1)
                PROSITE (2) -------------------------------BPTI_KUNITZ_1      ---------------------------------BPTI_KUNITZ_1      ----------------------------------------BPTI_KUNITZ_1      ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bd9 B   1 ISVCDLPADRGQCTAYIPQWFFAKTTEDCEKFVYGGCQGNANRFETKDDCIANCGCNLPSKVGPCRVSARMWFHNPETEKCEVFIYGGCHGNANRFATETECQEVCDRYQKPGFCYQPSETGPCKGSFPRYYYDYEDGECKEFIYGGCEGNANNFETKESCENAC 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Small proteins (3458)

Fold: BPTI-like (161)

Superfamily: BPTI-like (161)

Family: automated matches (24)

Protein domain: automated matches (24)

Sabellastarte magnifica [TaxId: 389514] (1)

1a	d4bd9b1	B:1-54
1b	d4bd9b2	B:55-109
1c	d4bd9b3	B:110-165

(no "CATH Domain" information available for 4BD9)

(no "Pfam Domain" information available for 4BD9)

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.

Chain B (PCPI_SABMA | P84875)

molecular function
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

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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	4bd9
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	CBPA4_HUMAN \| Q9UI42
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	PCPI_SABMA \| P84875
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	3.4.17.-
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UniProtKB/Swiss-Prot
	CBPA4_HUMAN \| Q9UI42	:	2bo9 2boa 2pcu 4a94

2bo9	HUMAN CARBOXYPEPTIDASE A4 IN COMPLEX WITH HUMAN LATEXIN.
2boa	HUMAN PROCARBOXYPEPTIDASE A4.
4a94	STRUCTURE OF THE CARBOXYPEPTIDASE INHIBITOR FROM NERITA VERSICOLOR IN COMPLEX WITH HUMAN CPA4

Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (10, 10)

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