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Title :   CRYSTAL STRUCTURE OF MOUSE CARNOSINASE CN2 COMPLEXED WITH MN AND BESTATIN

Authors :   H. Unno, T. Yamashita, N. Okumura, M. Kusunoki

Date :   14 May 08 (Deposition) - 10 Jun 08 (Release) - 02 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Metallopeptidase, Protein-Inhibitor Complex, Cndp2, Cndp Dipeptidase 2, Cn2, Bestatin, L-Carnosine, Carnosinase, Mn, Carboxypeptidase, Hydrolase, Metal-Binding, Metalloprotease, Protease, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Unno, T. Yamashita, S. Ujita, N. Okumura, H. Otani, A. Okumura, K. Nagai, M. Kusunoki
Structural Basis For Substrate Recognition And Hydrolysis By Mouse Carnosinase Cn2.
J. Biol. Chem. V. 283 27289 2008
PubMed-ID: 18550540 | Reference-DOI: 10.1074/JBC.M801657200

Molecule 1 - CYTOSOLIC NON-SPECIFIC DIPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.13.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CNDP2, CN2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CNDP DIPEPTIDASE 2, GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BES	2	Ligand/Ion	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:132 , GLU A:167 , HIS A:445	BINDING SITE FOR RESIDUE MN A 2001
2	AC2	SOFTWARE	HIS A:99 , ASP A:132 , ASP A:195	BINDING SITE FOR RESIDUE MN A 2002
3	AC3	SOFTWARE	ASP B:132 , GLU B:167 , HIS B:445	BINDING SITE FOR RESIDUE MN B 3001
4	AC4	SOFTWARE	HIS B:99 , ASP B:132 , ASP B:195	BINDING SITE FOR RESIDUE MN B 3002
5	AC5	SOFTWARE	HIS A:99 , ASP A:132 , GLU A:166 , GLU A:167 , ASP A:195 , TYR A:197 , ARG A:343 , GLU A:414 , GLY A:416 , SER A:417 , HIS A:445 , HIS B:228 , THR B:330	BINDING SITE FOR RESIDUE BES A 1080
6	AC6	SOFTWARE	HIS A:228 , THR A:330 , HIS B:99 , ASP B:132 , GLU B:166 , GLU B:167 , ASP B:195 , TYR B:197 , ARG B:343 , GLU B:414 , GLY B:416 , SER B:417 , HIS B:445	BINDING SITE FOR RESIDUE BES B 1081

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

Asymmetric/Biological Unit

No.	Residues
1	Asp A:132	-	Asp A:133
2	Asp B:132	-	Asp B:133

(no "SAP(SNP)/Variant" information available for 2ZOF)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARGE_DAPE_CPG2_2	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.	CNDP2_MOUSE	130-169	2	A:130-169 B:130-169

(no "Exon" information available for 2ZOF)

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 CNDP2_MOUSE | Q9D1A2 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:478
                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                |    6        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        
          CNDP2_MOUSE     - ----MSALKAVFQYIDENQDRYVKKLAEWVAIQSVSAWPEKRGEIRRMMEVAAADVQRLGGSVELVDIGKQKLPDGSEIPLPPILLGKLGSDPQKKTVCIYGHLDVQPAALEDGWDSEPFTLVEREGKLYGRGSTDDKGPVAGWMNALEAYQKTGQEIPVNLRFCLEGMEESGSEGLDELIFAQKDKFFKDVDYVCISDNYWLGKNKPCITYGLRGICYFFIEVECSDKDLHSGVYGGSVHEAMTDLISLMGCLVDKKGKILIPGINDAVAPVTDEEHALYDHIDFDMEEFAKDVGAETLLHSCKKDILMHRWRYPSLSLHGIEGAFSGSGAKTVIPRKVVGKFSIRLVPDMIPEVVSEQVSSYLSKKFAELQSPNKFKVYMGHGGKPWVSDFNHPHYQAGRRALKTVFGVEPDLTREGGSIPVTLTFQEATGKNVMLLPVGSADDGAHSQNEKLNRLNYIEGTKMLAAYLYEVSQLK 474
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...eee.....eee...eeeeee.......eeeeeee......hhhhh........ee...eee......hhhhhhhhhhhhhhhhh.......eeeeeee.hhhhh..hhhhhhhhhh........eeee...........eeeeee.eeeeeeeeee.....eehhhhh....hhhhhhhhhhh.........................hhhhhh...hhhhhhhhh........hhhhhhhhhhh..eeeeeeee..........ee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..ee.....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeee...............eeehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: A:130-169        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zof A  -3 SPNSMSALKAVFQYIDENQDRYVKKLAEWVAIQSVSAWPEKRGEIRRMMEVAAADVQRLGGSVELVDIGKQKLPDGSEIPLPPILLGKLGSDPQKKTVCIYGHLDVQPAALEDGWDSEPFTLVEREGKLYGRGSTDDKGPVAGWMNALEAYQKTGQEIPVNLRFCLEGMEESGSEGLDELIFAQKDKFFKDVDYVCISDNYWLGKNKPCITYGLRGICYFFIEVECSDKDLHSGVYGGSVHEAMTDLISLMGCLVDKKGKILIPGINDAVAPVTDEEHALYDHIDFDMEEFAKDVGAETLLHSCKKDILMHRWRYPSLSLHGIEGAFSGSGAKTVIPRKVVGKFSIRLVPDMIPEVVSEQVSSYLSKKFAELQSPNKFKVYMGHGGKPWVSDFNHPHYQAGRRALKTVFGVEPDLTREGGSIPVTLTFQEATGKNVMLLPVGSADDGAHSQNEKLNRLNYIEGTKMLAAYLYEVSQLK 474
                                     6        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

Chain B from PDB  Type:PROTEIN  Length:478
 aligned with CNDP2_MOUSE | Q9D1A2 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:478
                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                |    6        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        
          CNDP2_MOUSE     - ----MSALKAVFQYIDENQDRYVKKLAEWVAIQSVSAWPEKRGEIRRMMEVAAADVQRLGGSVELVDIGKQKLPDGSEIPLPPILLGKLGSDPQKKTVCIYGHLDVQPAALEDGWDSEPFTLVEREGKLYGRGSTDDKGPVAGWMNALEAYQKTGQEIPVNLRFCLEGMEESGSEGLDELIFAQKDKFFKDVDYVCISDNYWLGKNKPCITYGLRGICYFFIEVECSDKDLHSGVYGGSVHEAMTDLISLMGCLVDKKGKILIPGINDAVAPVTDEEHALYDHIDFDMEEFAKDVGAETLLHSCKKDILMHRWRYPSLSLHGIEGAFSGSGAKTVIPRKVVGKFSIRLVPDMIPEVVSEQVSSYLSKKFAELQSPNKFKVYMGHGGKPWVSDFNHPHYQAGRRALKTVFGVEPDLTREGGSIPVTLTFQEATGKNVMLLPVGSADDGAHSQNEKLNRLNYIEGTKMLAAYLYEVSQLK 474
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------Peptidase_M20-2zofB01 B:95-469                                                                                                                                                                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------Peptidase_M20-2zofB02 B:95-469                                                                                                                                                                                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-2zofB03 B:208-369                                                                                                                                       --------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-2zofB04 B:208-369                                                                                                                                       --------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...eee.....eee...eeeeee.......eeeeeee......hhhhh........ee...eee......hhhhhhhhhhhhhhhhh.......eeeeeee.hhhhh..hhhhhhhhh.........eeee...........eeeeee.eeeeeeeeee.....eehhhhh....hhhhhhhhhhh............hhhhhh.......hhhhhh...hhhhhhhhh........hhhhhhhhhhh..eeeeeeee..........ee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..ee.....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeee...............eeehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: B:130-169        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zof B  -3 SPNSMSALKAVFQYIDENQDRYVKKLAEWVAIQSVSAWPEKRGEIRRMMEVAAADVQRLGGSVELVDIGKQKLPDGSEIPLPPILLGKLGSDPQKKTVCIYGHLDVQPAALEDGWDSEPFTLVEREGKLYGRGSTDDKGPVAGWMNALEAYQKTGQEIPVNLRFCLEGMEESGSEGLDELIFAQKDKFFKDVDYVCISDNYWLGKNKPCITYGLRGICYFFIEVECSDKDLHSGVYGGSVHEAMTDLISLMGCLVDKKGKILIPGINDAVAPVTDEEHALYDHIDFDMEEFAKDVGAETLLHSCKKDILMHRWRYPSLSLHGIEGAFSGSGAKTVIPRKVVGKFSIRLVPDMIPEVVSEQVSSYLSKKFAELQSPNKFKVYMGHGGKPWVSDFNHPHYQAGRRALKTVFGVEPDLTREGGSIPVTLTFQEATGKNVMLLPVGSADDGAHSQNEKLNRLNYIEGTKMLAAYLYEVSQLK 474
                                     6        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

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 2ZOF)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MH (119)

Family: Peptidase_M20 (17)

Mus musculus (Mouse) (2)

1a	Peptidase_M20-2zofB01	B:95-469
1b	Peptidase_M20-2zofB02	B:95-469

Clan: no clan defined [family: M20_dimer] (13)

Family: M20_dimer (13)

Mus musculus (Mouse) (2)

2a	M20_dimer-2zofB03	B:208-369
2b	M20_dimer-2zofB04	B:208-369

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CNDP2_MOUSE | Q9D1A2)

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:0102008	cytosolic dipeptidase activity	Catalysis of the reaction: H2O + a dipeptide <=> 2 a standard alpha amino acid that occurs in the cytosol
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0034701	tripeptidase activity	Catalysis of the hydrolysis of a tripeptide.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:132 - Asp A:133	[ RasMol ]
		Asp B:132 - Asp B:133	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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