1QMU - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   DUCK CARBOXYPEPTIDASE D DOMAIN II

Authors :   F. X. Gomis-Rueth, M. Coll, F. X. Aviles, J. Vendrell, L. D. Fricker

Date :   06 Oct 99 (Deposition) - 13 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Carboxypeptidase, Hydrolase, Zinc-Dependent Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. X. Gomis-Rueth, V. Companys, Y. Qian, L. D. Fricker, J. Vendrell, F. X. Aviles, M. Coll
Crystal Structure Of Avian Carboxypeptidase D Domain Ii : A Prototype For The Regulatory Metallocarboxypeptidase Subfamily
Embo J. V. 18 5817 1999
PubMed-ID: 10545093 | Reference-DOI: 10.1093/EMBOJ/18.21.5817

Molecule 1 - CARBOXYPEPTIDASE GP180 RESIDUES 503-882
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	KM71
	Expression System Taxid	:	4922
	Fragment	:	YES
	Organ	:	LIVER
	Organism Common	:	CRESTED DUCK
	Organism Scientific	:	LOPHONETTA SPECULARIOIDES
	Organism Taxid	:	8836
	Other Details	:	OBTAINED AFTER CLONING INTO AND OVEREXPRESSION FROM A PICHIA PASTORIS SYSTEM.

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 33)

No.	Name	Count	Type	Full Name
1	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	9	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:132 , ASN A:136 , ASN A:140 , TYR A:141 , ASP A:142 , ASP A:156 , ASP A:328 , NAG A:902	BINDING SITE FOR RESIDUE NAG A 901
02	AC2	SOFTWARE	NAG A:901 , MAN A:903	BINDING SITE FOR RESIDUE NAG A 902
03	AC3	SOFTWARE	NAG A:902 , HOH A:2112	BINDING SITE FOR RESIDUE MAN A 903
04	AC4	SOFTWARE	ASN A:321 , NAG A:912 , HOH A:2092	BINDING SITE FOR RESIDUE NAG A 911
05	AC5	SOFTWARE	NAG A:911	BINDING SITE FOR RESIDUE NAG A 912
06	AC6	SOFTWARE	PHE A:309 , LEU A:311 , GLN A:375 , ASN A:377 , NAG A:922	BINDING SITE FOR RESIDUE NAG A 921
07	AC7	SOFTWARE	NAG A:921 , MAN A:923	BINDING SITE FOR RESIDUE NAG A 922
08	AC8	SOFTWARE	NAG A:922 , HOH A:2116	BINDING SITE FOR RESIDUE MAN A 923
09	AC9	SOFTWARE	LYS A:223 , LYS A:231 , HOH A:2120	BINDING SITE FOR RESIDUE SO4 A 996
10	BC1	SOFTWARE	ARG A:292 , ARG A:293	BINDING SITE FOR RESIDUE SO4 A 997
11	BC2	SOFTWARE	HIS A:74 , ARG A:135 , ASN A:144 , ARG A:145 , TYR A:250 , VAL A:252 , ZN A:999 , HOH A:2121	BINDING SITE FOR RESIDUE SO4 A 998
12	BC3	SOFTWARE	HIS A:74 , GLU A:77 , HIS A:181 , SO4 A:998 , HOH A:2121	BINDING SITE FOR RESIDUE ZN A 999

Asymmetric Unit

No.	Residues
1	A:230	-	A:275

Asymmetric Unit

No.	Residues
1	Pro A:190	-	Phe A:191

(no "SAP(SNP)/Variant" information available for 1QMU)

Asymmetric 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.	CBPD_LOPSP	62-84	1	A:65-87
1	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPD_ANAPL	130-152 564-586	1	- A:65-87
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPD_LOPSP	178-188	1	A:181-191
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPD_ANAPL	260-270 680-690	1	- A:181-191

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPD_LOPSP	62-84	3	A:65-87
1	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPD_ANAPL	130-152 564-586	3	- A:65-87
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPD_LOPSP	178-188	3	A:181-191
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPD_ANAPL	260-270 680-690	3	- A:181-191

(no "Exon" information available for 1QMU)

Asymmetric 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:380
 aligned with CBPD_ANAPL | Q90240 from UniProtKB/Swiss-Prot  Length:1389

    Alignment length:380
                                   512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882
           CBPD_ANAPL   503 QAVQPVDFRHHHFSDMEIFLRRYANEYPSITRLYSVGKSVELRELYVMEISDNPGIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNFGTDPEVTDLVQSTRIHIMPSMNPDGYEKSQEGDRGGTVGRNNSNNYDLNRNFPDQFFQVTDPPQPETLAVMSWLKTYPFVLSANLHGGSLVVNYPFDDDEQGIAIYSKSPDDAVFQQLALSYSKENKKMYQGSPCKDLYPTEYFPHGITNGAQWYNVPGGMQDWNYLNTNCFEVTIELGCVKYPKAEELPKYWEQNRRSLLQFIKQVHRGIWGFVLDATDGRGILNATISVADINHPVTTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQVNFTLSRT 882
               SCOP domains d1qmua2 A:4-304 Carboxypeptidase D, catalytic domain                                                                                                                                                                                                                                                         d1qmua1 A:305-383 Carboxypeptidase D C-terminal domain                          SCOP domains
               CATH domains 1qmuA01 A:4-304 Zn peptidases                                                                                                                                                                                                                                                                                1qmuA02 A:305-383  [code=2.60.40.1120, no name defined]                         CATH domains
               Pfam domains ---------------Peptidase_M14-1qmuA01 A:19-294                                                                                                                                                                                                                                                      ----------CarboxypepD_reg-1qmuA02 A:305-381                                            -- Pfam domains
     Sec.struct. author (1) ...........hhhhhhhhhhhhhhhh...eeeee..........eeeee...........eeeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh-----...hhhhhhh...................................hhhhhhhhhhhhhh.eeeeeeee..eeeeee................hhhhhhhhhhhhhh.hhhhhh............hhh.eeehhhhh....hhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhhhheeeeeeee..........eee..............eeee....eeeeeeee......eeeeeee....eee..eee... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------eeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------CARBOXYPEPT_ZN_1       ---------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmu A   4 QAVQPVDFRHHHFSDMEIFLRRYANEYPSITRLYSVGKSVELRELYVMEISDNPGIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNFGTDPEVTDLVQSTRIHIMPSMNPDGYEKSQEGDRGGTVGRNNSNNYDLNRNFPDQFFQVTDPPQPETLAVMSWLKTYPFVLSANLHGGSLVVNYPFDDDEQGIAIYSKSPDDAVFQQLALSYSKENKKMYQGSPCKDLYPTEYFPHGITNGAQWYNVPGGMQDWNYLNTNCFEVTIELGCVKYPKAEELPKYWEQNRRSLLQFIKQVHRGIWGFVLDATDGRGILNATISVADINHPVTTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQVNFTLSRT 383
                                    13        23        33        43        53        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       313       323       333       343       353       363       373       383

Chain A from PDB  Type:PROTEIN  Length:380
 aligned with CBPD_LOPSP | P83852 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:380
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380
           CBPD_LOPSP     1 QAVQPVDFRHHHFSDMEIFLRRYANEYPSITRLYSVGKSVELRELYVMEISDNPGIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNFGTDPEVTDLVQSTRIHIMPSMNPDGYEKSQEGDRGGTVGRNNSNNYDLNRNFPDQFFQVTDPPQPETLAVMSWLKTYPFVLSANLHGGSLVVNYPFDDDEQGIAIYSKSPDDAVFQQLALSYSKENKKMYQGSPCKDLYPTEYFPHGITNGAQWYNVPGGMQDWNYLNTNCFEVTIELGCVKYPKAEELPKYWEQNRRSLLQFIKQVHRGIWGFVLDATDGRGILNATISVADINHPVTTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQVNFTLSRT 380
               SCOP domains d1qmua2 A:4-304 Carboxypeptidase D, catalytic domain                                                                                                                                                                                                                                                         d1qmua1 A:305-383 Carboxypeptidase D C-terminal domain                          SCOP domains
               CATH domains 1qmuA01 A:4-304 Zn peptidases                                                                                                                                                                                                                                                                                1qmuA02 A:305-383  [code=2.60.40.1120, no name defined]                         CATH domains
               Pfam domains ---------------Peptidase_M14-1qmuA01 A:19-294                                                                                                                                                                                                                                                      ----------CarboxypepD_reg-1qmuA02 A:305-381                                            -- Pfam domains
     Sec.struct. author (1) ...........hhhhhhhhhhhhhhhh...eeeee..........eeeee...........eeeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh-----...hhhhhhh...................................hhhhhhhhhhhhhh.eeeeeeee..eeeeee................hhhhhhhhhhhhhh.hhhhhh............hhh.eeehhhhh....hhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhhhheeeeeeee..........eee..............eeee....eeeeeeee......eeeeeee....eee..eee... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------eeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------CARBOXYPEPT_ZN_1       ---------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmu A   4 QAVQPVDFRHHHFSDMEIFLRRYANEYPSITRLYSVGKSVELRELYVMEISDNPGIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNFGTDPEVTDLVQSTRIHIMPSMNPDGYEKSQEGDRGGTVGRNNSNNYDLNRNFPDQFFQVTDPPQPETLAVMSWLKTYPFVLSANLHGGSLVVNYPFDDDEQGIAIYSKSPDDAVFQQLALSYSKENKKMYQGSPCKDLYPTEYFPHGITNGAQWYNVPGGMQDWNYLNTNCFEVTIELGCVKYPKAEELPKYWEQNRRSLLQFIKQVHRGIWGFVLDATDGRGILNATISVADINHPVTTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQVNFTLSRT 383
                                    13        23        33        43        53        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       313       323       333       343       353       363       373       383

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: Zn peptidases (137)

Crested duck (Lophonetta specularioides) (2)

1qmuA01

A:4-304

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1120, no name defined] (4)

Crested duck (Lophonetta specularioides) (2)

1qmuA02

A:305-383

Asymmetric Unit(hide GO term definitions)

Chain A (CBPD_ANAPL | Q90240)

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:0004185	serine-type carboxypeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (CBPD_LOPSP | P83852)

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:0004185	serine-type carboxypeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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		Pro A:190 - Phe A:191	[ RasMol ]

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	1qmu
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(no "Related Entries Specified in the PDB File" available for 1QMU)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (2, 2)

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Related Entries Specified in the PDB File