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(-) Description

Title :  SERRATIA PROTEASE IN COMPLEX WITH INHIBITOR
 
Authors :  U. Baumann
Date :  20 Mar 97  (Deposition) - 25 Mar 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloprotease, Serralysin, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Baumann
Crystal Structure Of The 50 Kda Metallo Protease From S. Marcescens In Complex With The Synthetic Inhibitor Cbz-Leu-Ala-Nhoh
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERRATIA PROTEASE
    Chains: A
    EC Number: 3.4.24.40
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Other Details: PURCHASED FROM SIGMA
    Strain: NOT KNOWN, PROBABLY SM6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
10Z91Ligand/IonN-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-HYDROXY-L-ALANINAMIDE
2CA7Ligand/IonCALCIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:176 , HIS A:180 , HIS A:186 , 0Z9 A:674BINDING SITE FOR RESIDUE ZN A 472
02AC2SOFTWAREARG A:253 , GLY A:255 , THR A:257 , ASP A:285 , GLY A:287 , ASP A:290BINDING SITE FOR RESIDUE CA A 474
03AC3SOFTWAREGLY A:288 , ASP A:290 , THR A:327 , GLU A:329 , HOH A:2057 , HOH A:2059BINDING SITE FOR RESIDUE CA A 476
04AC4SOFTWAREGLY A:334 , GLY A:336 , ASP A:338 , GLY A:351 , ALA A:353 , ASP A:356BINDING SITE FOR RESIDUE CA A 478
05AC5SOFTWAREASN A:343 , ALA A:345 , ASN A:347 , GLY A:360 , GLY A:362 , ASP A:365BINDING SITE FOR RESIDUE CA A 480
06AC6SOFTWAREGLY A:352 , GLY A:354 , ASP A:356 , GLY A:369 , ALA A:371 , ASP A:374BINDING SITE FOR RESIDUE CA A 482
07AC7SOFTWAREGLY A:370 , GLY A:372 , ASP A:374 , ASP A:400 , HOH A:2081 , HOH A:2141BINDING SITE FOR RESIDUE CA A 484
08AC8SOFTWAREGLY A:361 , GLY A:362 , GLY A:363 , ASP A:365 , ASP A:383 , ASP A:390 , HOH A:2076BINDING SITE FOR RESIDUE CA A 486
09AC9SOFTWAREALA A:134 , TYR A:135 , ALA A:136 , LEU A:138 , HIS A:176 , GLU A:177 , HIS A:180 , HIS A:186 , ASN A:191 , ALA A:192 , TYR A:216 , ZN A:472BINDING SITE FOR RESIDUE 0Z9 A 674
10ACTAUTHORHIS A:176 , GLU A:177 , HIS A:180 , HIS A:186ACTIVE SITE, HISTIDINES ARE ZINC LIGANDS AND E 177 THE PUTATIVE CATALYTIC BASE. TYR 216 IS INVOLVED IN LIGAND BINDING.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AF0)

(-) 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 1AF0)

(-) 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:470
 aligned with PRZN_SERMA | P23694 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:470
                                    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       427       437       447       457       467       477       487
           PRZN_SERMA    18 ATTGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYNDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANPSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEANSSDFIHFVDHFSGTAGEALLSYNASSNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 487
               SCOP domains d1af0a2 A:2-246 Metalloprotease                                                                                                                                                                                                                      d1af0a1 A:247-471 Metalloprotease                                                                                                                                                                                                 SCOP domains
               CATH domains --1af0A01       1af0A02 A:18-249 Collagenase (Catalytic Domain)                                                                                                                                                                                         1af0A01 A:4-17,A:250-471 Alkaline Protease, subunit P, domain 1                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..................hhhhhhhh................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.hhhhhhh..................eeeeee....eeeeee.........eeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1af0 A   2 ATTGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGDPTYNDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFDKEANSSSFIHFVDHFSGTAGEALLSYNASSNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 471
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AF0)

(-) Gene Ontology  (12, 12)

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.

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 Related Entries

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

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

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