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Title :   A POLYMORPH OF CARBOXYPEPTIDASE B ZYMOGEN STRUCTURE

Authors :   D. Fernandez

Date :   12 Mar 09 (Deposition) - 20 Oct 09 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : A

Keywords :   Procarboxypeptidase B Cpb Zymogen Metalloprotease Polymorphic Form, Carboxypeptidase, Disulfide Bond, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Fernandez, E. Boix, I. Pallares, F. X. Aviles, J. Vendrell
Analysis Of A New Crystal Form Of Procarboxypeptidase B: Further Insights Into The Catalytic Mechanism
Biopolymers 2009
PubMed-ID: 19802820 | Reference-DOI: 10.1002/BIP.21320

Molecule 1 - CARBOXYPEPTIDASE B
	Chains	:	A
	EC Number	:	3.4.17.2
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9
	Expression System Strain	:	KM71
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	CPB1, CPB
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , HOH A:315	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	LEU A:187 , SER A:188 , ILE A:189 , LYS A:190 , GLY A:262 , ILE A:263 , HOH A:366 , HOH A:507	BINDING SITE FOR RESIDUE GOL A 309
3	AC3	SOFTWARE	HIS A:7 , TYR A:9 , GLN A:24 , HIS A:27A , GLU A:28A , SER A:31A	BINDING SITE FOR RESIDUE GOL A 310
4	AC4	SOFTWARE	SER A:27 , GLU A:28 , PRO A:30 , CYS A:152 , THR A:153 , THR A:154 , GLY A:155 , ALA A:156 , THR A:158 , HOH A:463	BINDING SITE FOR RESIDUE GOL A 311
5	AC5	SOFTWARE	LEU A:32 , ILE A:33 , SER A:34 , LYS A:51 , GLY A:53 , PRO A:55 , HOH A:523 , HOH A:582	BINDING SITE FOR RESIDUE GOL A 312
6	AC6	SOFTWARE	TYR A:299 , ASN A:302 , TYR A:303 , HOH A:571	BINDING SITE FOR RESIDUE GOL A 313

Asymmetric/Biological Unit

No.	Residues
1	A:66	-	A:79
2	A:138	-	A:161
3	A:152	-	A:166

Asymmetric/Biological Unit

No.	Residues
1	Lys A:39A	-	Pro A:40A
2	Ser A:197	-	Tyr A:198
3	Pro A:205	-	Tyr A:206
4	Arg A:272	-	Asp A:273

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

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.	CBPB1_PIG	167-189	1	A:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_PIG	304-314	1	A:196-206

(no "Exon" information available for 3GLJ)

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:395
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:395
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           CBPB1_PIG     22 FEGEKVFRVNVEDENDISLLHELASTRQIDFWKPDSVTQIKPHSTVDFRVKAEDILAVEDFLEQNELQYEVLINNLRSVLEAQFDSRVRTTGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d3glja1 A:7A-95A automated matches                                                       d3glja2 A:4-308 automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhhhhh.eeeee..hhhhh...eeeeeee...hhhhhhhhhhhh...eeeee.hhhhhhhhh................hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeee.hhh......hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3glj A   7A FEGEKVFRVNVEDENDISLLHELASTRQIDFWKPDSVTQIKPHSTVDFRVKAEDILAVEDFLEQNELQYEVLINNLRSVLEAQFDSRVRTTGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                            |||||||16A|||||||26A|||||||36A|||||||46A|||||||56A|||||||66A|||||||76A|||||||86A|||||||||4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    |  193       203       213       223       233       243       253       263       273       283       293       303     
                            ||||||15A||||||24A||||||33A||||||42A||||||51A||||||60A||||||69A||||||78A||||||87A||||||||4                                                                                                                                                                                     188A                                                                                                                        
                           7A||||||16A||||||25A||||||34A||||||43A||||||52A||||||61A||||||70A||||||79A||||||88A|||||||                                                                                                                                                                                                                                                                                                                  
                            8A||||||17A||||||26A||||||35A||||||44A||||||53A||||||62A||||||71A||||||80A||||||89A||||||                                                                                                                                                                                                                                                                                                                  
                             9A||||| 18A||||| 27A||||| 36A||||| 45A||||| 54A||||| 63A||||| 72A||||| 81A||||| 90A|||||                                                                                                                                                                                                                                                                                                                  
                             10A||||  19A||||  28A||||  37A||||  46A||||  55A||||  64A||||  73A||||  82A||||  91A||||                                                                                                                                                                                                                                                                                                                  
                              11A|||   20A|||   29A|||   38A|||   47A|||   56A|||   65A|||   74A|||   83A|||   92A|||                                                                                                                                                                                                                                                                                                                  
                               12A||    21A||    30A||    39A||    48A||    57A||    66A||    75A||    84A||    93A||                                                                                                                                                                                                                                                                                                                  
                                13A|     22A|     31A|     40A|     49A|     58A|     67A|     76A|     85A|     94A|                                                                                                                                                                                                                                                                                                                  
                                 14A      23A      32A      41A      50A      59A      68A      77A      86A      95A

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Protease propeptides/inhibitors (19)

Family: automated matches (1)

Protein domain: automated matches (1)

Pig (Sus scrofa) [TaxId: 9823] (1)

d3glja1

A:7A-95A

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Zn-dependent exopeptidases (214)

Family: Pancreatic carboxypeptidases (77)

Protein domain: automated matches (23)

Pig (Sus scrofa) [TaxId: 9823] (21)

d3glja2

A:4-308

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBPB1_PIG | P09955)

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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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 ]
		Lys A:39A - Pro A:40A	[ RasMol ]
		Pro A:205 - Tyr A:206	[ RasMol ]
		Ser A:197 - Tyr A:198	[ RasMol ]

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1nsa	THE SAME PROTEIN IN DIFFERENT SPACE GROUP AND CRYSTAL PACKING

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (3, 3)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (10, 10)

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