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Title :  CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (DVU_0896) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.75 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Mar 10  (Deposition) - 07 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Lipoprotein, Hydrolase, Sporulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase (Dvu_0896) From Desulfovibrio Vulgaris Hildenborough At 1. 75 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDVU_0896
    Organism ScientificDESULFOVIBRIO VULGARIS
    Organism Taxid882
    StrainHILDENBOROUGH / ATCC 29579 / NCIMB 8303
    SynonymLIPOPROTEIN, NLP/P60 FAMILY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 54)

Asymmetric/Biological Unit (5, 54)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL9Ligand/IonCHLORIDE ION
3GOL11Ligand/IonGLYCEROL
4MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5MSE30Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREACT A:13 , GLN A:182 , ARG A:183 , TRP A:324 , ASP A:332 , HOH A:548 , HOH A:631 , HOH A:950BINDING SITE FOR RESIDUE GOL A 1
02AC2SOFTWAREHOH A:26 , THR A:184 , ALA A:185 , TRP A:187 , SER A:335 , ARG A:338 , ASP A:339 , ARG A:350 , HOH A:465 , HOH A:557BINDING SITE FOR RESIDUE GOL A 3
03AC3SOFTWAREASP A:243 , HIS A:258 , GLN A:320 , GLU A:329 , ARG A:331 , HOH A:568 , ARG B:163BINDING SITE FOR RESIDUE GOL A 4
04AC4SOFTWARECL A:23 , HIS A:392 , MSE A:410 , TRP A:411 , GLY A:412 , ARG A:452 , HOH A:658 , HOH A:799BINDING SITE FOR RESIDUE GOL A 8
05AC5SOFTWAREGLU A:45 , GLY A:46 , ARG A:423 , TYR A:424 , VAL A:425 , HOH A:682 , HOH A:850 , LEU B:122BINDING SITE FOR RESIDUE GOL A 10
06AC6SOFTWAREGOL A:1 , CYS A:333 , SER A:334 , SER A:352 , HOH A:477BINDING SITE FOR RESIDUE ACT A 13
07AC7SOFTWAREGLY A:173 , PHE A:178 , MSE A:180 , TRP A:324 , ARG A:423 , HOH A:603 , HOH A:623 , HOH A:678 , HOH A:799BINDING SITE FOR RESIDUE MES A 14
08AC8SOFTWAREASP A:68 , ARG A:69BINDING SITE FOR RESIDUE CL A 17
09AC9SOFTWAREARG A:87 , TRP A:347 , PRO A:349 , HOH A:470BINDING SITE FOR RESIDUE CL A 18
10BC1SOFTWAREGLY A:173 , TRP A:411BINDING SITE FOR RESIDUE CL A 21
11BC2SOFTWAREGOL A:8 , ILE A:413 , ARG A:414 , ARG A:452 , HOH A:668BINDING SITE FOR RESIDUE CL A 23
12BC3SOFTWAREACT B:12 , GLN B:182 , ARG B:183 , TRP B:324 , ASP B:332 , ASN B:351 , HOH B:603 , HOH B:649BINDING SITE FOR RESIDUE GOL B 2
13BC4SOFTWAREHOH B:25 , THR B:184 , ALA B:185 , TRP B:187 , SER B:335 , ARG B:338 , ASP B:339 , ARG B:350 , HOH B:468 , HOH B:513BINDING SITE FOR RESIDUE GOL B 5
14BC5SOFTWAREARG A:163 , ASP B:242 , ASP B:243 , HIS B:258 , GLN B:320 , GLU B:329 , ARG B:331 , HOH B:575 , HOH B:624BINDING SITE FOR RESIDUE GOL B 6
15BC6SOFTWAREGLU B:45 , GLY B:46 , ARG B:423 , TYR B:424 , VAL B:425 , HOH B:824BINDING SITE FOR RESIDUE GOL B 7
16BC7SOFTWAREMES B:15 , HIS B:392 , MSE B:410 , TRP B:411 , GLY B:412 , LEU B:449 , ARG B:452 , HOH B:690 , HOH B:786BINDING SITE FOR RESIDUE GOL B 9
17BC8SOFTWAREGLN B:56 , ASP B:57 , ARG B:59 , ASP B:139 , TYR B:141 , ASN B:315 , HOH B:515BINDING SITE FOR RESIDUE GOL B 11
18BC9SOFTWAREGOL B:2 , CYS B:333 , SER B:334 , ASN B:351 , SER B:352 , HOH B:489BINDING SITE FOR RESIDUE ACT B 12
19CC1SOFTWAREGOL B:9 , GLY B:173 , PHE B:178 , TRP B:324 , TRP B:411 , ARG B:414 , ARG B:423 , HOH B:625 , HOH B:786BINDING SITE FOR RESIDUE MES B 15
20CC2SOFTWAREALA B:209 , TRP B:347BINDING SITE FOR RESIDUE CL B 16
21CC3SOFTWARELYS B:64 , HIS B:400 , GLU B:401BINDING SITE FOR RESIDUE CL B 19
22CC4SOFTWAREGLY B:437 , ASN B:443 , GLY B:448 , LEU B:449BINDING SITE FOR RESIDUE CL B 20
23CC5SOFTWAREGLY B:173 , TRP B:411 , ARG B:423BINDING SITE FOR RESIDUE CL B 22
24CC6SOFTWAREGLY B:66 , ALA B:67 , ASP B:68 , ARG B:69BINDING SITE FOR RESIDUE CL B 24

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M1U)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr A:141 -Pro A:142
2Tyr A:176 -Pro A:177
3Lys A:301 -Pro A:302
4Leu A:459 -Pro A:460
5Tyr B:141 -Pro B:142
6Tyr B:176 -Pro B:177
7Lys B:301 -Pro B:302
8Leu B:459 -Pro B:460

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M1U)

(-) Exons   (0, 0)

(no "Exon" information available for 3M1U)

(-) 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:425
 aligned with Q72DN3_DESVH | Q72DN3 from UniProtKB/TrEMBL  Length:464

    Alignment length:430
                                    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
         Q72DN3_DESVH    32 SRPATPPVTPPSREGHVADLDRFPQDLRVYAMKAGADRQLLPFTEQAAQDARWNRRFFAPWRMTRISVPVKDVAAPFGTDGRPRGYAENLLPWDVTRWGALASGAALDLYPSQAWKGIVVSNSALREVPTLRPMFTAPTRAGQGYPFDMFQRTAVWMGTPVFVGHATADRAWLYVETAFAAGWMPAADVARVDDAFMTRYESGSLAAILRDDTSLNGADGTHLATAHIGTVLPLSGASQVGRTVLVPVRAPEGHAVVVPVLLTSGEAAQKPVPLTPGNMAELGNRMMGQPYGWGGLYEDRDCSSTLRDLFTPFGLWLPRNSASQAKAGRYVDIAKLDADDKEARIVAEGVPFMTLLWLRGHITLYLGLHEGQAAMFHNMWGIRTHRGGVEGRYVLGRAVVTSTRPGLDVPGNDNADGLLGRMQGMSILPG 461
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeee...eeee........................eeeee....eeeeeee.....eeeee....eeeee...eee.hhhhhhhhhh..eeee....eeee.....eeeee....eee..-----.eeeeeeee.....eeeeeeee....eee.....hhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhh..eeee....hhhhhhhhhhhhh....eeeee..eeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee..............hhhhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m1u A  32 SRPATPPVTPPSREGHVADLDRFPQDLRVYAmKAGADRQLLPFTEQAAQDARWNRRFFAPWRmTRISVPVKDVAAPFGTDGRPRGYAENLLPWDVTRWGALASGAALDLYPSQAWKGIVVSNSALREVPTLRPmFTAPTRAGQGYPFDmFQRTAVWmGTPVFVGHATADRAWLYVETAFAAGWmPAADVARVDDAFmTRYESGSLAAILRDDTSLNGADGTHLATAHIGTVLPLS-----GRTVLVPVRAPEGHAVVVPVLLTSGEAAQKPVPLTPGNmAELGNRmmGQPYGWGGLYEDRDCSSTLRDLFTPFGLWLPRNSASQAKAGRYVDIAKLDADDKEARIVAEGVPFmTLLWLRGHITLYLGLHEGQAAmFHNmWGIRTHRGGVEGRYVLGRAVVTSTRPGLDVPGNDNADGLLGRmQGmSILPG 461
                                    41        51        61 |      71        81        91  |    101       111       121       131       141       151       161   |   171       181      |191       201       211   |   221      |231       241       251       261    |    -|      281       291       301       311     ||321       331       341       351       361       371       381  |    391       401    |  411       421       431       441       451 |  |  461
                                                          63-MSE                         94-MSE                                                                165-MSE        180-MSE 188-MSE                    215-MSE      228-MSE                               266   272                                   310-MSE  ||                                                               384-MSE               406-MSE                                        453-MSE    
                                                                                                                                                                                                                                                                                                                       317-MSE                                                                                      410-MSE                                       456-MSE 
                                                                                                                                                                                                                                                                                                                        318-MSE                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:420
 aligned with Q72DN3_DESVH | Q72DN3 from UniProtKB/TrEMBL  Length:464

    Alignment length:420
                                    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
         Q72DN3_DESVH    42 PSREGHVADLDRFPQDLRVYAMKAGADRQLLPFTEQAAQDARWNRRFFAPWRMTRISVPVKDVAAPFGTDGRPRGYAENLLPWDVTRWGALASGAALDLYPSQAWKGIVVSNSALREVPTLRPMFTAPTRAGQGYPFDMFQRTAVWMGTPVFVGHATADRAWLYVETAFAAGWMPAADVARVDDAFMTRYESGSLAAILRDDTSLNGADGTHLATAHIGTVLPLSGASQVGRTVLVPVRAPEGHAVVVPVLLTSGEAAQKPVPLTPGNMAELGNRMMGQPYGWGGLYEDRDCSSTLRDLFTPFGLWLPRNSASQAKAGRYVDIAKLDADDKEARIVAEGVPFMTLLWLRGHITLYLGLHEGQAAMFHNMWGIRTHRGGVEGRYVLGRAVVTSTRPGLDVPGNDNADGLLGRMQGMSILPG 461
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) N_NLPC_P60-3m1uB05 B:42-141                                                                         ----------------------SH3_6-3m1uB03 B:164-217                               ------SH3_7-3m1uB07 B:224-272                          ----------------------------------------------NLPC_P60-3m1uB01 B:319-431                                                                                       ------------------------------ Pfam domains (1)
           Pfam domains (2) N_NLPC_P60-3m1uB06 B:42-141                                                                         ----------------------SH3_6-3m1uB04 B:164-217                               ------SH3_7-3m1uB08 B:224-272                          ----------------------------------------------NLPC_P60-3m1uB02 B:319-431                                                                                       ------------------------------ Pfam domains (2)
         Sec.struct. author .......hhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeee...eeee........................eeeee....eeeeeee.....eeeee....eeeee...eee.hhhhhhhhhh..eeee....eeee.....eeeee....eeeeeee...eeeeeeeee.....eeeeeeeee...eee.....hhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeee....hhhhhhhhhhhhh....eeeee..eeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee..............hhhhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m1u B  42 PSREGHVADLDRFPQDLRVYAmKAGADRQLLPFTEQAAQDARWNRRFFAPWRmTRISVPVKDVAAPFGTDGRPRGYAENLLPWDVTRWGALASGAALDLYPSQAWKGIVVSNSALREVPTLRPmFTAPTRAGQGYPFDmFQRTAVWmGTPVFVGHATADRAWLYVETAFAAGWmPAADVARVDDAFmTRYESGSLAAILRDDTSLNGADGTHLATAHIGTVLPLSGASQVGRTVLVPVRAPEGHAVVVPVLLTSGEAAQKPVPLTPGNmAELGNRmmGQPYGWGGLYEDRDCSSTLRDLFTPFGLWLPRNSASQAKAGRYVDIAKLDADDKEARIVAEGVPFmTLLWLRGHITLYLGLHEGQAAmFHNmWGIRTHRGGVEGRYVLGRAVVTSTRPGLDVPGNDNADGLLGRmQGmSILPG 461
                                    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
                                                63-MSE                         94-MSE                                                                165-MSE        180-MSE 188-MSE                    215-MSE      228-MSE                                                                           310-MSE  ||                                                               384-MSE               406-MSE                                        453-MSE    
                                                                                                                                                                                                                                                                                                             317-MSE                                                                                      410-MSE                                       456-MSE 
                                                                                                                                                                                                                                                                                                              318-MSE                                                                                                                                           

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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  (0, 0)

(no "SCOP Domain" information available for 3M1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M1U)

(-) Pfam Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3M1U)

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