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(-) Description

Title :  DUCK CARBOXYPEPTIDASE D DOMAIN II IN COMPLEX WITH GEMSA
 
Authors :  F. X. Gomis-Rueth, M. Coll, F. X. Aviles, J. Vendrell, L. D. Fricker
Date :  09 Feb 01  (Deposition) - 08 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Carboxypeptidase, Hydrolase, Zinc-Dependent Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Aloy, V. Companys, J. Vendrell, F. X. Aviles, L. D. Fricker, M. Coll, F. X. Gomis-Rueth
The Crystal Structure Of The Inhibitor-Complexed Carboxypeptidase D Domain Ii And The Modeling Of Regulatory Carboxypeptidases
J. Biol. Chem. V. 276 16177 2001
PubMed-ID: 11278909  |  Reference-DOI: 10.1074/JBC.M011457200
(for further references see the PDB file header)

(-) Compounds

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 BY OVEREXPRESSION FROM A PICHIA PASTORIS SYSTEM.
    Strain: KM71

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GEM1Ligand/Ion(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5SO41Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:132 , ASN A:136 , ASN A:140 , TYR A:141 , ASP A:142 , ASP A:156 , NAG A:902BINDING SITE FOR RESIDUE NAG A 901
2AC2SOFTWAREASP A:156 , NAG A:901 , BMA A:903BINDING SITE FOR RESIDUE NAG A 902
3AC3SOFTWARENAG A:902 , HOH A:2187 , HOH A:2188BINDING SITE FOR RESIDUE BMA A 903
4AC4SOFTWAREASN A:321 , THR A:323 , HOH A:2189 , HOH A:2191BINDING SITE FOR RESIDUE NAG A 911
5AC5SOFTWAREPHE A:309 , LEU A:311 , GLN A:375 , ASN A:377 , NAG A:922BINDING SITE FOR RESIDUE NDG A 921
6AC6SOFTWARENDG A:921 , HOH A:2193BINDING SITE FOR RESIDUE NAG A 922
7AC7SOFTWAREARG A:292 , ARG A:293 , HOH A:2056BINDING SITE FOR RESIDUE SO4 A 998
8AC8SOFTWAREHIS A:74 , GLU A:77 , HIS A:181 , GEM A:801BINDING SITE FOR RESIDUE ZN A 999
9AC9SOFTWAREHIS A:74 , GLU A:77 , ARG A:135 , ASN A:144 , ARG A:145 , HIS A:181 , GLY A:182 , ASN A:188 , ASP A:192 , GLY A:246 , TRP A:249 , TYR A:250 , VAL A:252 , GLU A:272 , ZN A:999BINDING SITE FOR RESIDUE GEM A 801

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:230 -A:275

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:190 -Phe A:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H8L)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPD_LOPSP62-84  1A:65-87
CBPD_ANAPL130-152
564-586		  1-
A:65-87
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPD_LOPSP178-188  1A:181-191
CBPD_ANAPL260-270
680-690		  1-
A:181-191

(-) Exons   (0, 0)

(no "Exon" information available for 1H8L)

(-) Sequences/Alignments

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: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 d1h8la2 A:4-304 Carboxypeptidase D, catalytic domain                                                                                                                                                                                                                                                         d1h8la1 A:305-383 Carboxypeptidase D C-terminal domain                          SCOP domains
               CATH domains 1h8lA01 A:4-304 Zn peptidases                                                                                                                                                                                                                                                                                1h8lA02 A:305-383  [code=2.60.40.1120, no name defined]                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee............eeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhh..................hhhhh............hhhhhhhhhhhhhh.eeeeeeee..eeeeee................hhhhhhhhhhhhhh.hhhhhh............hhh.eeehhhhh....hhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..........eeee..eeeeee.....eeee....eeeeeeee......eeeeeee....eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------CARBOXYPEPT_ZN_1       ---------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8l 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 d1h8la2 A:4-304 Carboxypeptidase D, catalytic domain                                                                                                                                                                                                                                                         d1h8la1 A:305-383 Carboxypeptidase D C-terminal domain                          SCOP domains
               CATH domains 1h8lA01 A:4-304 Zn peptidases                                                                                                                                                                                                                                                                                1h8lA02 A:305-383  [code=2.60.40.1120, no name defined]                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee............eeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhh..................hhhhh............hhhhhhhhhhhhhh.eeeeeeee..eeeeee................hhhhhhhhhhhhhh.hhhhhh............hhh.eeehhhhh....hhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..........eeee..eeeeee.....eeee....eeeeeeee......eeeeeee....eee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------CARBOXYPEPT_ZN_1       ---------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8l 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H8L)

(-) Gene Ontology  (12, 22)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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  1h8l
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  CBPD_ANAPL | Q90240
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  CBPD_LOPSP | P83852
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CBPD_ANAPL | Q90240: 1qmu
        CBPD_LOPSP | P83852: 1qmu

(-) Related Entries Specified in the PDB File

1qmu DUCK CARBOXYPEPTIDASE D DOMAIN II