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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF MANNOSE-BINDING LECTIN-ASSOCIATED SERINE PROTEINASE-3 REVEALS THE STRUCTURAL BASIS FOR ENZYME INACTIVITY ASSOCIATED WITH THE 3MC SYNDROME
 
Authors :  T. Yongqing, P. G. Wilmann, S. B. Reeve, T. H. Coetzer, A. I. Smith, J. C. W R. N. Pike, L. C. Wijeyewickrema
Date :  05 May 13  (Deposition) - 03 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protease, Chymotrypsin Fold, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yongqing, P. G. Wilmann, S. B. Reeve, T. H. Coetzer, A. I. Smith, J. C. Whisstock, R. N. Pike, L. C. Wijeyewickrema
The X-Ray Crystal Structure Of Mannose-Binding Lectin-Associated Serine Proteinase-3 Reveals The Structura Basis For Enzyme Inactivity Associated With The Carnevale, Mingarelli, Malpuech, And Michels (3Mc) Syndrome.
J. Biol. Chem. V. 288 22399 2013
PubMed-ID: 23792966  |  Reference-DOI: 10.1074/JBC.M113.483875

(-) Compounds

Molecule 1 - MANNAN-BINDING LECTIN SERINE PROTEASE 1
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CRARF, CRARF1, MASP1, PRSS5
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COMPLEMENT FACTOR MASP-3, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR, MANNOSE-BINDING LECTIN-ASSOCIATED SERINE PROTEASE 1, MASP-1, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE, RA- REACTIVE FACTOR SERINE PROTEASE P100, RARF, SERINE PROTEASE 5, MANNAN-BINDING LECTIN SERINE PROTEASE 1 HEAVY CHAIN, MANNAN-BINDING LECTIN SERINE PROTEASE 1 LIGHT CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:439 , LEU B:443 , LEU B:460 , PHE B:461 , TRP B:678BINDING SITE FOR RESIDUE IMD B 801

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:301 -A:349
2A:329 -A:362
3A:367 -A:414
4A:397 -A:432
5A:436 -A:573
6A:630 -A:649
7A:660 -A:692
8B:301 -B:349
9B:329 -B:362
10B:367 -B:414
11B:397 -B:432
12B:436 -B:573
13B:630 -B:649
14B:660 -B:692

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:313 -Pro A:314
2Glu A:399 -Pro A:400
3Val A:475 -Pro A:476
4Leu A:717 -Pro A:718
5Glu B:313 -Pro B:314
6Glu B:399 -Pro B:400
7Val B:475 -Pro B:476
8Ser B:638 -Gly B:639

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KKD)

(-) 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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee........eeee.....ee...eeeeee...eeeee..eee.eeeee............eeee...........eeeee...........eeeeee....eee.hhh..eeee.....ee..........eee.....................eeeeeeee......eeeeeeeeeee..eeeehhhhhh...........hhh.eeeee...........eeeeeeeeee.............eeeee...........................eeeeee.......eeeeeeeehhhhhhhhh.........eeee..............eeeee......eeeeeeeee............eeeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kkd A 298 GNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNNNTGIYTCSAQGVWMNKVLGRSLPTCLPECGQPSRSLPGRNAEPGLFPWQALIVVEDTSRVPNDKWFGSGALLSASWILTAAHVLRSQRRDTTVIPVSKEHVTVYLGLHDVRDKSGAVNSSAARVVLHPDFNIQNYNHDIALVQLQEPVPLGPHVMPVCLPRLEPEGPAPHMLGLVAGWGLSDVLQYVKLPVVPHAECKTSYESRYSVTENMFCAGYYEKDTCLGDSGEAFVIFDDLSQRWVVQGLVSWGGPEECGSKQVYGVYTKVSNYVDWVWEQMGLP 718
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437      |455       465       475       485       495       505       515       525       535       545       555       565       575       585       613       623       633   ||  646       658       668       678       688       698       708       718
                                                                                                                                                                            444|                                                                                                                                          594|                     637|          654|                                                             
                                                                                                                                                                             453                                                                                                                                           613                      641           657                                                             


Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eeee.....ee...eeeeee...eeeee..eee.eeeee............eeee...........eeeee...........eeeeee....eee....eeee.....ee..........eee...................ee........eeeeeeee......eeeeeeeee....eeeehhhhhh...........hhh.eeeee......hhhhheeeeeeeeee.............eeeee...........................eeeeeeee.....eeeeeeeeeeeeehhhhhhhhhhh..........eeee................eeeeee....eeeeeeeeee............eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kkd B 298 GNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNTGIYTCSAQGVWMNKVLGRSLPTCLPECGQPSRSLPSLVQRIIGGRNAEPGLFPWQALIVVEDTSRVPNDKWFGSGALLSASWILTAAHVLRSQRRDTTVIPVSKEHVTVYLGLHDVRDKSGAVNSSAARVVLHPDFNIQNYNHDIALVQLQEPVPLGPHVMPVCLPRLEPEGPAPHMLGLVAGWGISNRTLSDVLQYVKLPVVPHAECKTSYESRSGNYSVTENMFCAGYYEGGKDTCLGDSGEAFVIFDDLSQRWVVQGLVSWGGPEECGSKQVYGVYTKVSNYVDWVWEQMGL 717
                                   307       317       327       337       347       357       367       377       387       397       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       612       622       632       642       652       662       672       682       692       702       712     
                                                                                                                                      406|                                                                                                                                                                                         597|                                                                                                          
                                                                                                                                       409                                                                                                                                                                                          611
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

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    Glu B:399 - Pro B:400   [ RasMol ]  
    Leu A:717 - Pro A:718   [ RasMol ]  
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        MASP1_HUMAN | P48740: 3dem 3gov 4aqb 4djz 4igd 4iw4

(-) Related Entries Specified in the PDB File

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