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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INACTIVE MUTANT OF MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A FLUOROGENIC SYNTHETIC PEPTIDIC SUBSTRATE
 
Authors :  E. A. Stura, L. Vera, E. Cassar-Lajeunesse, I. Tranchant, M. Amoura, V.
Date :  06 Mar 13  (Deposition) - 12 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Keywords :  Hydrolase Substrate Complex, Zincin-Like, Gelatinase, Collagenase, Catalytic Domain, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Tranchant, L. Vera, B. Czarny, M. Amoura, E. Cassar, F. Beau, E. A. Stura, V. Dive
Halogen Bonding Controls Selectivity Of Fret Substrate Probes For Mmp-9.
Chem. Biol. V. 21 408 2014
PubMed-ID: 24583051  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.01.008

(-) Compounds

Molecule 1 - FLUOROGENIC PEPTIDIC SUBSTRATE (8MC)PLG(PHI)(DNW)AR(NH2)
    Chains: P, Q
    Engineered: YES
    Other Details: FLUOROGENIC SYNTHETIC L-PEPTIDE SUBSTRATE WITH MMP-9 SPECIFICITY.
    Synthetic: YES
 
Molecule 2 - MATRIX METALLOPROTEINASE-9
    Chains: A, B
    EC Number: 3.4.24.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-14B
    Expression System Strain: BL21 (DE3 STAR)
    Expression System Taxid: 562
    Expression System Vector Type: PT7 PROMOTER
    Gene: CLG4B, MMP9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MMP-9, 92 KDA GELATINASE, 92 KDA TYPE IV COLLAGENASE, GELATINASE B, GELB, 67 KDA MATRIX METALLOPROTEINASE-9, 82 KDA MATRIX METALLOPROTEINASE-9

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABPQ
Biological Unit 1 (1x): A P 
Biological Unit 2 (1x):  B Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 29)

Asymmetric Unit (12, 29)
No.NameCountTypeFull Name
18MC2Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI2Ligand/IonAZIDE ION
3CA2Ligand/IonCALCIUM ION
4DNW2Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO4Ligand/Ion1,2-ETHANEDIOL
6GOL2Ligand/IonGLYCEROL
7NH22Mod. Amino AcidAMINO GROUP
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PGO2Ligand/IonS-1,2-PROPANEDIOL
10PHI2Mod. Amino AcidIODO-PHENYLALANINE
11SR4Ligand/IonSTRONTIUM ION
12ZN4Ligand/IonZINC ION
Biological Unit 1 (9, 10)
No.NameCountTypeFull Name
18MC1Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI1Ligand/IonAZIDE ION
3CA-1Ligand/IonCALCIUM ION
4DNW1Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7NH21Mod. Amino AcidAMINO GROUP
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PGO1Ligand/IonS-1,2-PROPANEDIOL
10PHI1Mod. Amino AcidIODO-PHENYLALANINE
11SR-1Ligand/IonSTRONTIUM ION
12ZN-1Ligand/IonZINC ION
Biological Unit 2 (8, 9)
No.NameCountTypeFull Name
18MC1Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI1Ligand/IonAZIDE ION
3CA-1Ligand/IonCALCIUM ION
4DNW1Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7NH21Mod. Amino AcidAMINO GROUP
8PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
9PGO1Ligand/IonS-1,2-PROPANEDIOL
10PHI1Mod. Amino AcidIODO-PHENYLALANINE
11SR-1Ligand/IonSTRONTIUM ION
12ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:189 , HIS A:190 , HIS A:226 , ALA A:227 , HIS A:230 , ZN A:302 , LEU P:3 , GLY P:4 , PHI P:5BINDING SITE FOR RESIDUE AZI A 301
02AC2SOFTWAREHIS A:226 , HIS A:230 , HIS A:236 , AZI A:301 , GLY P:4BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREHIS A:175 , ASP A:177 , HIS A:190 , HIS A:203BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:418 , HOH A:455 , HOH A:565BINDING SITE FOR RESIDUE SR A 305
06AC6SOFTWAREASP A:131 , ASP A:206 , GLU A:208 , PGO A:307 , HOH A:434BINDING SITE FOR RESIDUE SR A 306
07AC7SOFTWAREASP A:131 , GLY A:197 , ASP A:206 , ASP A:207 , GLU A:208 , LEU A:209 , SR A:306 , HOH A:424 , HOH A:457 , HOH A:532 , HOH A:551 , HOH A:569BINDING SITE FOR RESIDUE PGO A 307
08AC8SOFTWAREHIS A:266 , GLY A:269 , HOH A:539 , GLY B:106 , PHE B:107BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWARELEU A:187 , HIS A:190 , HOH A:413BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREVAL A:216 , GLY A:217 , TYR A:248 , HOH A:437BINDING SITE FOR RESIDUE PEG A 310
11BC2SOFTWARELEU A:114 , GLY A:233 , HOH A:428 , HOH A:430 , HOH A:548BINDING SITE FOR RESIDUE GOL A 311
12BC3SOFTWAREALA B:189 , HIS B:190 , HIS B:226 , ALA B:227 , HIS B:230 , ZN B:301 , LEU Q:3 , GLY Q:4 , PHI Q:5BINDING SITE FOR RESIDUE AZI Q 101
13BC4SOFTWAREHIS B:226 , HIS B:230 , HIS B:236 , GLY Q:4 , AZI Q:101BINDING SITE FOR RESIDUE ZN B 301
14BC5SOFTWAREHIS B:175 , ASP B:177 , HIS B:190 , HIS B:203BINDING SITE FOR RESIDUE ZN B 302
15BC6SOFTWAREASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208BINDING SITE FOR RESIDUE CA B 303
16BC7SOFTWAREALA B:164 , ASP B:165 , GLY B:197 , GLN B:199 , ASP B:201 , HOH B:451 , HOH B:455BINDING SITE FOR RESIDUE SR B 304
17BC8SOFTWAREASP B:131 , ASP B:206 , GLU B:208 , PGO B:306 , HOH B:422BINDING SITE FOR RESIDUE SR B 305
18BC9SOFTWAREASP B:131 , ASP B:206 , ASP B:207 , GLU B:208 , SR B:305 , HOH B:423 , HOH B:573BINDING SITE FOR RESIDUE PGO B 306
19CC1SOFTWAREHIS B:117 , HOH B:523BINDING SITE FOR RESIDUE EDO B 307
20CC2SOFTWARETYR B:245 , MET B:247 , HOH B:593 , ARG Q:8BINDING SITE FOR RESIDUE EDO B 308
21CC3SOFTWAREGLY B:217 , TYR B:218 , HOH B:576BINDING SITE FOR RESIDUE GOL B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JIJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JIJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JIJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JIJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4JIJ)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee...............eeeee..........eeee....ee......eehhhhhhhhhhhhh........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jij A 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHAFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee...............eeeee..........eeee....ee......eehhhhhhhhhhhhh........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jij B 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHAFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    


Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4jij P   1 xPLGfaARx   9
                            |   ||  |
                            1-8MC|  |
                                5-PHI
                                 6-DNW
                                    9-NH2


Chain Q from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4jij Q   1 xPLGfaARx   9
                            |   ||  |
                            |   ||  |
                            1-8MC|  |
                                5-PHI
                                 6-DNW
                                    9-NH2
   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  (0, 0)

(no "SCOP Domain" information available for 4JIJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JIJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JIJ)

(-) Gene Ontology  (38, 38)

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  4jij
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  MMP9_HUMAN | P14780
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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP9_HUMAN | P14780: 1gkc 1gkd 1itv 1l6j 1lkg 2ovx 2ovz 2ow0 2ow1 2ow2 4h1q 4h2e 4h3x 4h82 4hma 4jqg 4wzv 4xct 5cuh 5i12 5th6 5th9

(-) Related Entries Specified in the PDB File

2ow0 MMP-9 ACTIVE SITE MUTANT WITH IODINE-LABELED CARBOXYLATE INHIBITOR
2ow1 MMP-9 ACTIVE SITE MUTANT WITH TRIFLUOROMETHYL HYDROXAMATE INHIBITOR
4h1q CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4h2e CRYSTALCRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS
4h3x CRYSTAL STRUCTURE OF AN MMP BROAD SPECTRUM HYDROXAMATE BASED INHIBITOR CC27 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
4h82 CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4hma CRYSTAL STRUCTURE OF AN MMP TWIN CARBOXYLATE BASED INHIBITOR LC20 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
4jqg
4jxa