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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CARBOXYPEPTIDASE M
 
Authors :  K. Maskos, D. Reverter, W. Bode
Date :  17 Feb 04  (Deposition) - 08 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Metallopeptidase, Carboxypeptidase, Gpi-Anchor, Metalloprotease, Zinc, Lipoprotein, Hydrolase, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Reverter, K. Maskos, F. Tan, R. Skidgel, W. Bode
Crystal Structure Of Human Carboxypeptidase M, A Membrane-Bound Enzyme That Regulates Peptide Hormone Activity
J. Mol. Biol. V. 338 257 2004
PubMed-ID: 15066430  |  Reference-DOI: 10.1016/J.JMB.2004.02.058

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE M
    ChainsA
    EC Number3.4.17.12
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPVL1393
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:47 , ASN A:98 , NAG A:1404BINDING SITE FOR RESIDUE NAG A1403
2AC2SOFTWARENAG A:1403 , HOH A:2024 , HOH A:2025BINDING SITE FOR RESIDUE NAG A1404
3AC3SOFTWAREHIS A:66 , GLU A:69 , HIS A:173BINDING SITE FOR RESIDUE ZN A1405

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:121 -A:268
2A:225 -A:267
3A:324 -A:393

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:182 -Phe A:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048600R24HCBPM_HUMANPolymorphism7978197AR7H
2UniProtVAR_048601V133ICBPM_HUMANPolymorphism7309831AV116I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPM_HUMAN74-96  1A:57-79
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPM_HUMAN190-200  1A:173-183

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003383561ENSE00000937238chr12:69326664-69326458207CBPM_HUMAN1-54541A:1-3737
1.2ENST000003383562ENSE00000937239chr12:69279669-6927957298CBPM_HUMAN54-86331A:37-6933
1.3ENST000003383563ENSE00000937240chr12:69265736-69265564173CBPM_HUMAN87-144581A:70-12758
1.4ENST000003383564ENSE00000937241chr12:69264179-69263995185CBPM_HUMAN144-206631A:127-18963
1.5ENST000003383565ENSE00000937242chr12:69263275-69263105171CBPM_HUMAN206-263581A:189-24658
1.6ENST000003383566ENSE00000937243chr12:69260828-69260676153CBPM_HUMAN263-314521A:246-29752
1.7ENST000003383567ENSE00000920723chr12:69252851-69252703149CBPM_HUMAN314-363501A:297-34650
1.8ENST000003383568ENSE00001207135chr12:69250459-692449605500CBPM_HUMAN364-443801A:347-403 (gaps)57

(-) 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:394
 aligned with CBPM_HUMAN | P14384 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:403
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417   
           CBPM_HUMAN    18 LDFNYHRQEGMEAFLKTVAQNYSSVTHLHSIGKSVKGRNLWVLVVGRFPKEHRIGIPEFKYVANMHGDETVGRELLLHLIDYLVTSDGKDPEITNLINSTRIHIMPSMNPDGFEAVKKPDCYYSIGRENYNQYDLNRNFPDAFEYNNVSRQPETVAVMKWLKTETFVLSANLHGGALVASYPFDNGVQATGALYSRSLTPDDDVFQYLAHTYASRNPNMKKGDECKNKMNFPNGVTNGYSWYPLQGGMQDYNYIWAQCFEITLELSCCKYPREEKLPSFWNNNKASLIEYIKQVHLGVKGQVFDQNGNPLPNVIVEVQDRKHICPYRTNKYGEYYLLLLPGSYIINVTVPGHDPHITKVIIPEKSQNFSALKKDILLPFQGQLDSIPVSNPSCPMIPLYRNLP 420
               SCOP domains d1uwya2 A:1-296 Carboxypeptidase M, catalytic domain                                                                                                                                                                                                                                                    d1uwya1 A:297-403 Carboxypeptidase M C-terminal domain                                                      SCOP domains
               CATH domains 1uwyA01 A:1-296 Zn peptidases                                                                                                                                                                                                                                                                           1uwyA02 A:297-403  [code=2.60.40.1120, no name defined]                                                     CATH domains
               Pfam domains ----------Peptidase_M14-1uwyA01 A:11-286                                                                                                                                                                                                                                                      ----------CarboxypepD_reg-1uwyA02 A:297-370                                         --------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee............eeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhh..................................hhhhhhhhhhhhhh.eee..eee..eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhh...................eee.........hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..........eeee...............eeee....eeeeeeee......eeeeeee.........ee..ee.....---------............. Sec.struct. author
                 SAPs(SNPs) ------H------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBOXYPEPT_ZN_1       ---------------------------------------------------------------------------------------------CARBOXYPEPT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-37 UniProt: 1-54  --------------------------------Exon 1.3  PDB: A:70-127 UniProt: 87-144                   -------------------------------------------------------------Exon 1.5  PDB: A:189-246 UniProt: 206-263                 --------------------------------------------------Exon 1.7  PDB: A:297-346 UniProt: 314-363         Exon 1.8  PDB: A:347-403 (gaps) UniProt: 364-443          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.2  PDB: A:37-69           ---------------------------------------------------------Exon 1.4  PDB: A:127-189 UniProt: 144-206                      --------------------------------------------------------Exon 1.6  PDB: A:246-297 UniProt: 263-314           ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1uwy A   1 LDFNYHRQEGMEAFLKTVAQNYSSVTHLHSIGKSVKGRNLWVLVVGRFPKEHRIGIPEFKYVANMHGDETVGRELLLHLIDYLVTSDGKDPEITNLINSTRIHIMPSMNPDGFEAVKKPDCYYSIGRENYNQYDLNRNFPDAFEYNNVSRQPETVAVMKWLKTETFVLSANLHGGALVASYPFDNGVQATGALYSRSLTPDDDVFQYLAHTYASRNPNMKKGDECKNKMNFPNGVTNGYSWYPLQGGMQDYNYIWAQCFEITLELSCCKYPREEKLPSFWNNNKASLIEYIKQVHLGVKGQVFDQNGNPLPNVIVEVQDRKHICPYRTNKYGEYYLLLLPGSYIINVTVPGHDPHITKVIIPEKSQNFSALKKDILLPFQG---------PSCPMIPLYRNLP 403
                                    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|        -|      400   
                                                                                                                                                                                                                                                                                                                                                                                                                      381       391            

   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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPM_HUMAN | P14384)
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:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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.
    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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