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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN SERRATIA MARCESCENS METALLO-PROTEASE AND AN INHIBITOR FROM ERWINIA CHRYSANTHEMI
 
Authors :  U. Baumann, M. Bauer, S. Letoffe, P. Delepelaire, C. Wandersman
Date :  13 Jan 95  (Deposition) - 03 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Complex (Metalloprotease/Inhibitor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Baumann, M. Bauer, S. Letoffe, P. Delepelaire, C. Wandersman
Crystal Structure Of A Complex Between Serratia Marcescens Metallo-Protease And An Inhibitor From Erwinia Chrysanthemi.
J. Mol. Biol. V. 248 653 1995
PubMed-ID: 7752231  |  Reference-DOI: 10.1006/JMBI.1995.0249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERRATIA METALLO PROTEINASE
    Chains: A
    EC Number: 3.4.24.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: INH
    Expression System Plasmid: PUC
    Expression System Taxid: 562
    Gene: INH
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
 
Molecule 2 - ERWINIA CHRYSANTHEMI INHIBITOR
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: INH
    Expression System Plasmid: PUC
    Expression System Taxid: 562
    Gene: INH
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:176 , HIS A:180 , HIS A:186 , SER I:1BINDING SITE FOR RESIDUE ZN A 472
2AC2SOFTWAREARG A:253 , GLY A:255 , THR A:257 , ASP A:285 , GLY A:287 , ASP A:290BINDING SITE FOR RESIDUE CA A 473
3AC3SOFTWAREGLY A:288 , ASP A:290 , THR A:327 , GLU A:329 , HOH A:524 , HOH A:618BINDING SITE FOR RESIDUE CA A 474
4AC4SOFTWAREGLY A:334 , GLY A:336 , ASP A:338 , GLY A:351 , ALA A:353 , ASP A:356BINDING SITE FOR RESIDUE CA A 475
5AC5SOFTWAREASN A:343 , ALA A:345 , ASN A:347 , GLY A:360 , GLY A:362 , ASP A:365BINDING SITE FOR RESIDUE CA A 476
6AC6SOFTWAREGLY A:352 , GLY A:354 , ASP A:356 , GLY A:369 , ALA A:371 , ASP A:374BINDING SITE FOR RESIDUE CA A 477
7AC7SOFTWAREGLY A:361 , GLY A:362 , GLY A:363 , ASP A:365 , ASP A:383 , ASP A:390BINDING SITE FOR RESIDUE CA A 478
8AC8SOFTWAREGLY A:370 , GLY A:372 , ASP A:374 , GLN A:396 , ASP A:400 , HOH A:512BINDING SITE FOR RESIDUE CA A 479

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1I:24 -I:46

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SMP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.PRZN_SERMA189-198  1A:173-182
2HEMOLYSIN_CALCIUMPS00330 Hemolysin-type calcium-binding region signature.PRZN_SERMA372-390  1A:356-374

(-) Exons   (0, 0)

(no "Exon" information available for 1SMP)

(-) 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:468
 aligned with PRZN_SERMA | P23694 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:468
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479        
           PRZN_SERMA    20 TGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYNDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANPSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEANSSDFIHFVDHFSGTAGEALLSYNASSNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 487
               SCOP domains d1smpa2 A:4-246 Metalloprotease                                                                                                                                                                                                                    d1smpa1 A:247-471 Metalloprotease                                                                                                                                                                                                 SCOP domains
               CATH domains 1smpA01       1smpA02 A:18-249 Collagenase (Catalytic Domain)                                                                                                                                                                                         1smpA01 A:4-17,A:250-471 Alkaline Protease, subunit P, domain 1                                                                                                                                                                CATH domains
           Pfam domains (1) ---------------------------------------------------------------Peptidase_M10-1smpA01 A:67-209                                                                                                                 -----------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_M10_C-1smpA06 A:248-471                                                                                                                                                                                                Pfam domains (5)
         Sec.struct. author .hhhhhhhhhh.................hhhhhhhhh...............eeeee......................hhhhhhhhhhhhhhhhh..eeeee.........eeeee.............eee..............eeeee...hhhh.....hhhhhhhhhhhhhhh................hhh.................hhhh.............hhhhhhhhhhh...........eee.......hhh..........eee.......eee........eee...............eee.......eee......eee......eee......eee......eee......eee...hhhh.....eee........eee.hhhhhh..................eeeeeee....eeeeeee........eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1smp A   4 TGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYNDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEANSSDFIHFVDHFSGTAGEALLSYNASSNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 471
                                    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       393       403       413       423       433       443       453       463        


Chain I from PDB  Type:PROTEIN  Length:100
 aligned with INH_DICCH | P18958 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:100
                                    29        39        49        59        69        79        89        99       109       119
            INH_DICCH    20 SSLRLPSAAELSGQWVLSGAEQHCDIRLNTDVLDGTTWKLAGDTACLQKLLPEAPVGWRPTPDGLTLTQADGSAVAFFSRNRDRYEHKLVDGSVRTLKKK 119
               SCOP domains d1smpi_ I: Metalloprotease inhibitor                                                                 SCOP domains
               CATH domains 1smpI00 I:1-100  [code=2.40.128.10, no name defined]                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhh.eeeeee....eeeeee...........eee.hhhhhhh......eeee...eeeee.....eeeeeeee..eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1smp I   1 SSLRLPSAAELSGQWVLSGAEQHCDIRLNTDVLDGTTWKLAGDTACLQKLLPEAPVGWRPTPDGLTLTQADGSAVAFFSRNRDRYEHKLVDGSVRTLKKK 100
                                    10        20        30        40        50        60        70        80        90       100
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)
(-)
Clan: no clan defined [family: HemolysinCabind] (16)
(-)
Clan: no clan defined [family: Peptidase_M10_C] (10)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRZN_SERMA | P23694)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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: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.

Chain I   (INH_DICCH | P18958)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1smp
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  PRZN_SERMA | P23694
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRZN_SERMA | P23694: 1af0 1sat 4i35 5d7w

(-) Related Entries Specified in the PDB File

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