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(-) Description

Title :  CRYSTAL STRUCTURE OF A M20A METALLO PEPTIDASE (DAPE, LPG0809) FROM LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Oct 10  (Deposition) - 17 Nov 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metal Binding, Merops M20 Familiy, Phosphorylase/Hydrolase-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A M20A Metallo Peptidase (Dape, Lpg0809) From Legionella Pneumophila Subsp. Pneumophila Str Philadelphia 1 At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPE, LPG0809
    Organism Scientific: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1
    Organism Taxid: 272624
    Strain: PHILADELPHIA 1 / ATCC 33152 / DSM 7513

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 39)

Asymmetric Unit (6, 39)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2GOL10Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4MSE15Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 54)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL20Ligand/IonGLYCEROL
3IMD2Ligand/IonIMIDAZOLE
4MSE30Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:96 , ASP A:129 , GLU A:162 , ASP A:190 , ZN A:502 , HOH A:926BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREASP A:129 , GLU A:163 , HIS A:442 , ZN A:501 , GOL A:518 , HOH A:926BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREHIS A:52 , ASP A:264 , CL A:507 , CL A:508BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREGLU A:410 , CL A:505 , IMD A:513 , HOH A:1002BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWARESER A:226 , ARG A:305 , GLU A:410 , GLY A:411 , ZN A:504 , IMD A:513 , HOH A:941BINDING SITE FOR RESIDUE CL A 505
06AC6SOFTWARESER A:224 , ASN A:327 , VAL A:328 , HIS A:442 , HOH A:692BINDING SITE FOR RESIDUE CL A 506
07AC7SOFTWAREHIS A:52 , ASP A:264 , ZN A:503BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWAREGLN A:48 , HIS A:52 , ASP A:264 , ZN A:503BINDING SITE FOR RESIDUE CL A 508
09AC9SOFTWAREPHE A:424 , PRO A:425 , LYS A:426 , HOH A:681BINDING SITE FOR RESIDUE CL A 509
10BC1SOFTWAREHIS A:223 , ARG A:340 , THR A:413 , HOH A:692BINDING SITE FOR RESIDUE CL A 510
11BC2SOFTWAREGLY A:105 , TRP A:106 , HOH A:823 , HOH A:890BINDING SITE FOR RESIDUE CL A 511
12BC3SOFTWAREASP A:37 , ALA A:38BINDING SITE FOR RESIDUE CL A 512
13BC4SOFTWAREHIS A:223 , SER A:226 , GLU A:410 , LEU A:435 , ZN A:504 , CL A:505 , GOL A:518 , HOH A:555BINDING SITE FOR RESIDUE IMD A 513
14BC5SOFTWAREGLN A:269 , GLN A:272 , TYR A:407 , HOH A:601 , HOH A:627BINDING SITE FOR RESIDUE PEG A 514
15BC6SOFTWAREGLN A:240 , ASN A:249 , PRO A:363 , TYR A:364 , HOH A:712BINDING SITE FOR RESIDUE GOL A 515
16BC7SOFTWARETHR A:250 , GLY A:251 , GLU A:252 , ASN A:304 , ARG A:308 , HOH A:540 , HOH A:580 , HOH A:666 , HOH A:1034BINDING SITE FOR RESIDUE GOL A 516
17BC8SOFTWARELYS A:58 , GLU A:68 , ILE A:69 , HOH A:664 , HOH A:998BINDING SITE FOR RESIDUE GOL A 517
18BC9SOFTWAREASP A:190 , HIS A:223 , GLU A:410 , GLY A:412 , ILE A:414 , LEU A:435 , HIS A:442 , ZN A:502 , IMD A:513 , HOH A:768 , HOH A:926BINDING SITE FOR RESIDUE GOL A 518
19CC1SOFTWARELYS A:177 , GLU A:178 , GLY A:181 , GLN A:423 , HOH A:545 , HOH A:788BINDING SITE FOR RESIDUE GOL A 519
20CC2SOFTWAREGLY A:165 , SER A:166 , GLY A:375 , GLY A:376 , SER A:377 , HOH A:613 , HOH A:714 , HOH A:964BINDING SITE FOR RESIDUE GOL A 520
21CC3SOFTWARESER A:107 , LEU A:110 , LYS A:118BINDING SITE FOR RESIDUE GOL A 521
22CC4SOFTWAREHIS A:438 , HIS A:449 , HOH A:706 , HOH A:833 , HOH A:868BINDING SITE FOR RESIDUE GOL A 522
23CC5SOFTWAREHIS A:35 , SER A:164 , TYR A:167 , HOH A:835BINDING SITE FOR RESIDUE GOL A 523
24CC6SOFTWAREGLU A:41 , GLU A:42 , TYR A:259 , CYS A:260 , ASP A:261 , HOH A:910 , HOH A:991BINDING SITE FOR RESIDUE GOL A 524

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PFE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:129 -Asp A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PFE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PFE)

(-) Exons   (0, 0)

(no "Exon" information available for 3PFE)

(-) 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:471
 aligned with Q5ZXC3_LEGPH | Q5ZXC3 from UniProtKB/TrEMBL  Length:471

    Alignment length:471
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                             |       9        19        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 
         Q5ZXC3_LEGPH     - -MFKPQGLYDYICQQWQEEILPSLCDYIKIPNKSPHFDAKWEEHGYMEQAVNHIANWCKSHAPKGMTLEIVRLKNRTPLLFMEIPGQIDDTVLLYGHLDKQPEMSGWSDDLHPWKPVLKNGLLYGRGGADDGYSAYASLTAIRALEQQGLPYPRCILIIEACEESGSYDLPFYIELLKERIGKPSLVICLDSGAGNYEQLWMTTSLRGNLVGKLTVELINEGVHSGSASGIVADSFRVARQLISRIEDENTGEIKLPQLYCDIPDERIKQAKQCAEILGEQVYSEFPWIDSAKPVIQDKQQLILNRTWRPALTVTGADGFPAIADAGNVMRPVTSLKLSMRLPPLVDPEAASVAMEKALTQNPPYNAKVDFKIQNGGSKGWNAPLLSDWLAKAASEASMTYYDKPAAYMGEGGTIPFMSMLGEQFPKAQFMITGVLGPHSNAHGPNEFLHLDMVKKLTSCVSYVLYSFSQK 470
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------Peptidase_M20-3pfeA01 A:92-466                                                                                                                                                                                                                                                                                                                                                         ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-3pfeA02 A:203-366                                                                                                                                         -------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhh.....eeeee.......eeeeee...eeeeeeeeee...................eee..eee.......hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhh..hhhhhhhhhhhhhh...eeeee..........eeeeee.eeeeeeeeee......hhhhhh....hhhhhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..eeeeeeee..............eeeeeeeeee....hhhhhhhhhhhhhhh.hhhhheeeeee.......ee....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeeee..............eeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfe A   0 GmFKPQGLYDYICQQWQEEILPSLCDYIKIPNKSPHFDAKWEEHGYmEQAVNHIANWCKSHAPKGmTLEIVRLKNRTPLLFmEIPGQIDDTVLLYGHLDKQPEmSGWSDDLHPWKPVLKNGLLYGRGGADDGYSAYASLTAIRALEQQGLPYPRCILIIEACEESGSYDLPFYIELLKERIGKPSLVICLDSGAGNYEQLWmTTSLRGNLVGKLTVELINEGVHSGSASGIVADSFRVARQLISRIEDENTGEIKLPQLYCDIPDERIKQAKQCAEILGEQVYSEFPWIDSAKPVIQDKQQLILNRTWRPALTVTGADGFPAIADAGNVmRPVTSLKLSmRLPPLVDPEAASVAmEKALTQNPPYNAKVDFKIQNGGSKGWNAPLLSDWLAKAASEASmTYYDKPAAYmGEGGTIPFmSmLGEQFPKAQFmITGVLGPHSNAHGPNEFLHLDmVKKLTSCVSYVLYSFSQK 470
                             |       9        19        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 
                             |                                           46-MSE             65-MSE          81-MSE               103-MSE                                                                                           201-MSE                                                                                                                         329-MSE   339-MSE        354-MSE                                     398-MSE   408-MSE  417-MSE      430-MSE               452-MSE              
                             1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                           419-MSE
   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 3PFE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PFE)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)
(-)
Clan: no clan defined [family: M20_dimer] (13)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5ZXC3_LEGPH | Q5ZXC3)
molecular function
    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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  3pfe
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 Related Entries

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