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(-) Description

Title :  A DUAL INHIBITOR OF THE LEUKOCYTE PROTEASES CATHEPSIN G AND CHYMASE WITH THERAPEUTIC EFFICACY IN ANIMALS MODELS OF INFLAMMATION
 
Authors :  L. De Garavilla, M. N. Greco, E. C. Giardino, G. I. Wells, B. J. Haertlei J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, W. M. Abraha N. Sukumar, Z. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, P. Andrade B. P. Damiano, B. E. Maryanoff, P. J. B. Pereira, Z. M. Wang, H. Rubin, R. W. Bode, N. M. Schechter, S. Strobl
Date :  23 Apr 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Human Chymase, Serine Proteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. De Garavilla, M. N. Greco, N. Sukumar, Z. W. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, E. C. Giardino, G. I. Wells, B. J. Haertlein, J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, B. P. Damiano, P. Andrade-Gordon, B. E. Maryanoff
A Novel, Potent Dual Inhibitor Of The Leukocyte Proteases Cathepsin G And Chymase: Molecular Mechanisms And Anti-Inflammatory Activity In Vivo.
J. Biol. Chem. V. 280 18001 2005
PubMed-ID: 15741158  |  Reference-DOI: 10.1074/JBC.M501302200

(-) Compounds

Molecule 1 - CHYMASE
    ChainsA
    EC Number3.4.21.39
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneCMA1, CYM, CYH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAST CELL PROTEASE I

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OHH1Ligand/Ion2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5SO47Ligand/IonSULFATE ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OHH1Ligand/Ion2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5SO47Ligand/IonSULFATE ION
Biological Unit 2 (4, 24)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OHH2Ligand/Ion2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5SO414Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:72 , THR A:74 , GLU A:75 , THR A:154 , NAG A:303BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARENAG A:301BINDING SITE FOR RESIDUE NAG A 303
03AC3SOFTWAREASN A:95 , HOH A:1123 , HOH A:1214 , HOH A:1215 , HOH A:1219BINDING SITE FOR RESIDUE NAG A 302
04AC4SOFTWARELEU A:114 , THR A:115 , LEU A:116BINDING SITE FOR RESIDUE SO4 A 902
05AC5SOFTWAREPHE A:41 , ARG A:143 , PRO A:150 , GLY A:151 , HOH A:1187 , HOH A:1197BINDING SITE FOR RESIDUE SO4 A 903
06AC6SOFTWARELYS A:93 , HIS A:100 , HIS A:101 , HOH A:1070 , HOH A:1193BINDING SITE FOR RESIDUE SO4 A 904
07AC7SOFTWAREMET A:135 , ARG A:161 , ASN A:185 , LYS A:186 , HOH A:1072 , HOH A:1218BINDING SITE FOR RESIDUE SO4 A 905
08AC8SOFTWAREPRO A:38 , SER A:39 , ARG A:174BINDING SITE FOR RESIDUE SO4 A 906
09AC9SOFTWARETHR A:20 , GLU A:21BINDING SITE FOR RESIDUE SO4 A 907
10BC1SOFTWAREARG A:137 , ALA A:202 , HOH A:1125 , HOH A:1175BINDING SITE FOR RESIDUE SO4 A 908
11BC2SOFTWAREHIS A:25 , GLU A:78 , HOH A:1002 , HOH A:1005BINDING SITE FOR RESIDUE CO A 909
12BC3SOFTWARELYS A:40 , HIS A:57 , GLN A:166 , PRO A:185A , ARG A:185B , ALA A:190 , PHE A:191 , LYS A:192 , GLY A:193 , SER A:195 , SER A:214 , TYR A:215 , GLY A:216 , ARG A:217 , SER A:218 , ALA A:226 , HOH A:1040 , HOH A:1046 , HOH A:1107 , HOH A:1154 , HOH A:1209 , HOH A:1216BINDING SITE FOR RESIDUE OHH A 901
13BC4SOFTWARETYR A:32 , GLU A:34 , THR A:67 , ILE A:73 , TRP A:80 , LYS A:82 , HOH A:1034 , HOH A:1085 , HOH A:1130BINDING SITE FOR RESIDUE MES A 910

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:224 -Pro A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011770G46RCMA1_HUMANPolymorphism5246AG37R
2UniProtVAR_011771H66RCMA1_HUMANPolymorphism5247AH57R
3UniProtVAR_029190R98HCMA1_HUMANPolymorphism13306252AR90H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011770G46RCMA1_HUMANPolymorphism5246AG37R
2UniProtVAR_011771H66RCMA1_HUMANPolymorphism5247AH57R
3UniProtVAR_029190R98HCMA1_HUMANPolymorphism13306252AR90H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011770G46RCMA1_HUMANPolymorphism5246AG37R
2UniProtVAR_011771H66RCMA1_HUMANPolymorphism5247AH57R
3UniProtVAR_029190R98HCMA1_HUMANPolymorphism13306252AR90H

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CMA1_HUMAN22-245  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CMA1_HUMAN62-67  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CMA1_HUMAN197-208  1A:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CMA1_HUMAN22-245  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CMA1_HUMAN62-67  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CMA1_HUMAN197-208  1A:189-200
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CMA1_HUMAN22-245  2A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CMA1_HUMAN62-67  2A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CMA1_HUMAN197-208  2A:189-200

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002503781ENSE00001144725chr14:24977471-2497738488CMA1_HUMAN1-20200--
1.2aENST000002503782aENSE00001144738chr14:24976712-24976562151CMA1_HUMAN20-70511A:16-6149
1.3ENST000002503783ENSE00000586440chr14:24975810-24975675136CMA1_HUMAN70-115461A:61-107 (gaps)48
1.4aENST000002503784aENSE00000654524chr14:24975488-24975234255CMA1_HUMAN116-200851A:108-192 (gaps)88
1.5bENST000002503785bENSE00001816406chr14:24974865-24974561305CMA1_HUMAN201-247471A:193-245 (gaps)53

(-) Sequences/Alignments

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
(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:226
 aligned with CMA1_HUMAN | P23946 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:226
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          CMA1_HUMAN     22 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQFNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGVAQGIVSYGRSDAKPPAVFTRISHYRPWINQILQAN  247
               SCOP domains d1t31a_ A: Chymase (mast cell protease I)                                                                                                                                                                                          SCOP domains
               CATH domains 1t31A01     1t31A02 A:28-120,A:233-245 Trypsin-like serine proteases                                       1t31A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                   1t31A02       CATH domains
               Pfam domains Trypsin-1t31A01 A:16-238                                                                                                                                                                                                   ------- Pfam domains
         Sec.struct. author ....ee........eeeeeee......eeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh.........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------R-------------------R-------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 22-245                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:16-61 UniProt: 20-70           ---------------------------------------------Exon 1.4a  PDB: A:108-192 (gaps) UniProt: 116-200                                    Exon 1.5b  PDB: A:193-245 (gaps)                Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3  PDB: A:61-107 (gaps) UniProt: 70-115------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1t31 A   16 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQKNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGAAQGIVSYGRSDAKPPAVFTRISHYQPWINQILQAN  245
                                    25        35 |||    42        52        63        73 ||  |  83        93       103       113       123       133       143    || 154       164    || 176 |     185||     193       207       217   ||  229       239      
                                               36A||                       61|          75|  |                                                                  148|                169|  177A     185A|              202|           221|                     
                                                36B|                        63           77  |                                                                   150                 172            185B               207            224                     
                                                 36C                                       79A                                                                                                                                                                

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (CMA1_HUMAN | P23946)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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: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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in 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).
biological process
    GO:0002003    angiotensin maturation    The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
    GO:0071333    cellular response to glucose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0050720    interleukin-1 beta biosynthetic process    The chemical reactions and pathways resulting in the formation of interleukin-1 beta.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    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:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    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.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CMA1_HUMAN | P239461klt 1nn6 1pjp 2hvx 3n7o 3s0n 4afq 4afs 4afu 4afz 4ag1 4ag2 4k2y 4k5z 4k60 4k69 4kp0

(-) Related Entries Specified in the PDB File

1pjp THE 2.2 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH SUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYLKETONE: STRUCTURAL EXPLANATION FOR ITS DIPEPTIDYL CARBOXYPEPTIDASE SPECIFICITY.