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(-) Description

Title :  CRYSTAL STRUCTURE OF A XAA-PRO DIPEPTIDASE WITH BOUND METHIONINE IN THE ACTIVE SITE
 
Authors :  D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  30 Jul 07  (Deposition) - 21 Aug 07  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Biol. Unit 3:  A,B  (4x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Amidohydrolase, Dipeptidase, Tim Barrel, Protein Structure Initiative, Psi-2, 9355E, Nysgxrc, Structural Genomics, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Xiang, C. Xu, D. Kumaran, A. C. Brown, J. M. Sauder, S. K. Burley, S. Swaminathan, F. M. Raushel
Functional Annotation Of Two New Carboxypeptidases From The Amidohydrolase Superfamily Of Enzymes.
Biochemistry V. 48 4567 2009
PubMed-ID: 19358546  |  Reference-DOI: 10.1021/BI900453U

(-) Compounds

Molecule 1 - XAA-PRO DIPEPTIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ALTEROMONAS MACLEODII
    Organism Taxid: 28108

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B
Biological Unit 3 (4x): AB
Biological Unit 4 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1MET2Ligand/IonMETHIONINE
2MG2Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 52)
No.NameCountTypeFull Name
1MET4Ligand/IonMETHIONINE
2MG-1Ligand/IonMAGNESIUM ION
3MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 52)
No.NameCountTypeFull Name
1MET4Ligand/IonMETHIONINE
2MG-1Ligand/IonMAGNESIUM ION
3MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 104)
No.NameCountTypeFull Name
1MET8Ligand/IonMETHIONINE
2MG-1Ligand/IonMAGNESIUM ION
3MSE96Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 26)
No.NameCountTypeFull Name
1MET2Ligand/IonMETHIONINE
2MG-1Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , HIS A:71 , ASP A:328 , HOH A:677 , HOH A:751BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWAREHIS B:69 , HIS B:71 , LYS B:194 , ASP B:328 , HOH B:768 , HOH B:834BINDING SITE FOR RESIDUE MG B 500
3AC3SOFTWAREHIS A:150 , VAL A:201 , LEU A:202 , HIS A:235 , HIS A:237 , THR A:277 , ALA A:280 , GLY A:281 , ILE A:309 , ASP A:328 , HOH A:751BINDING SITE FOR RESIDUE MET A 600
4AC4SOFTWAREHIS B:150 , VAL B:201 , LEU B:202 , HIS B:235 , HIS B:237 , HIS B:255 , THR B:277 , ALA B:280 , GLY B:281 , ILE B:309 , ASP B:328 , HOH B:834BINDING SITE FOR RESIDUE MET B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QS8)

(-) Exons   (0, 0)

(no "Exon" information available for 2QS8)

(-) 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:406
 aligned with K7N5L1_ALTMA | K7N5L1 from UniProtKB/TrEMBL  Length:418

    Alignment length:406
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406      
         K7N5L1_ALTMA     7 SKTLIHAGKLIDGKSDQVQSRISIVIDGNIISDIKKGFISSNDFEDYIDLRDHTVLPGLMDMHVHFGQEYQSKAQAPIKVEREMQAILATQHAYVTFKSGFTTVRQVGDSGLVAISLRDAINSGKLAGPRIFAAGKTIATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQFTQEEVDAVVSAAKDYGMWVAVHAHGAEGMKRAIKAGVDSIEHGTFMDLEAMDLMIENGTYYVPTISAGEFVAEKSKIDNFFPEIVRPKAASVGPQISDTFRKAYEKGVKIAFGTDAGVQKHGTNWKEFVYMVENGMPAMKAIQSATMETAKLLRIEDKLGSIESGKLADLIAVKGNPIEDISVLENVDVVIKDGLLYEG 412
               SCOP domains d2qs8a1 A:7-63,A:374-412 Xaa-Pro dipeptidase             d2qs8a2 A:64-373 Xaa-Pro dipeptidase                                                                                                                                                                                                                                                                                  d2qs8a1 A:7-63,A:374-412                SCOP domains
               CATH domains 2qs8A01 A:7-65,A:373-412 Urease, subunit C, domain 1       -2qs8A02 A:67-372 Metal-dependent hydrolases                                                                                                                                                                                                                                                                       2qs8A01 A:7-65,A:373-412                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........eeeeeeeee..eeeeeee.........eeeeeeeeeeee.eeeeee................hhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhh......eeee.....ee...........hhhhh...hhhh.ee.hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhh..hhhhhhhhhhhhhhhhh................eeee......hhhhhh.eeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qs8 A   7 SKTLIHAGKLIDGKSDQVQSRISIVIDGNIISDIKKGFISSNDFEDYIDLRDHTVLPGLmDmHVHFGQEYQSKAQAPIKVEREmQAILATQHAYVTFKSGFTTVRQVGDSGLVAISLRDAINSGKLAGPRIFAAGKTIATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQFTQEEVDAVVSAAKDYGmWVAVHAHGAEGmKRAIKAGVDSIEHGTFmDLEAmDLmIENGTYYVPTISAGEFVAEKSKIDNFFPEIVRPKAASVGPQISDTFRKAYEKGVKIAFGTDAGVQKHGTNWKEFVYmVENGmPAmKAIQSATmETAKLLRIEDKLGSIESGKLADLIAVKGNPIEDISVLENVDVVIKDGLLYEG 412
                                    16        26        36        46        56        66 |      76        86   |    96       106       116       126       136       146       156       166       176       186       196       206       216       226   |   236     | 246       256  |    266|      276       286       296       306       316       326       336       346  |  | 356   |   366       376       386       396       406      
                                                                                      66-MSE                  90-MSE                                                                                                                                     230-MSE     242-MSE          259-MSE|  |                                                                          344-MSE|  |     360-MSE                                                
                                                                                        68-MSE                                                                                                                                                                                             264-MSE                                                                              349-MSE                                                           
                                                                                                                                                                                                                                                                                              267-MSE                                                                              352-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with K7N5L1_ALTMA | K7N5L1 from UniProtKB/TrEMBL  Length:418

    Alignment length:405
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     
         K7N5L1_ALTMA     6 DSKTLIHAGKLIDGKSDQVQSRISIVIDGNIISDIKKGFISSNDFEDYIDLRDHTVLPGLMDMHVHFGQEYQSKAQAPIKVEREMQAILATQHAYVTFKSGFTTVRQVGDSGLVAISLRDAINSGKLAGPRIFAAGKTIATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQFTQEEVDAVVSAAKDYGMWVAVHAHGAEGMKRAIKAGVDSIEHGTFMDLEAMDLMIENGTYYVPTISAGEFVAEKSKIDNFFPEIVRPKAASVGPQISDTFRKAYEKGVKIAFGTDAGVQKHGTNWKEFVYMVENGMPAMKAIQSATMETAKLLRIEDKLGSIESGKLADLIAVKGNPIEDISVLENVDVVIKDGLLY 410
               SCOP domains d2qs8b1 B:6-63,B:374-410 Xaa-Pro dipeptidase              d2qs8b2 B:64-373 Xaa-Pro dipeptidase                                                                                                                                                                                                                                                                                  d2qs8b1 B:6-63,B:374-410              SCOP domains
               CATH domains 2qs8B01 B:6-65,B:373-410 Urease, subunit C, domain 1        -2qs8B02 B:67-372 Metal-dependent hydrolases                                                                                                                                                                                                                                                                       2qs8B01 B:6-65,B:373-410               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee........eeeeeeeee..eeeeeee.........eeeeeeeeeeee.eeeeee................hhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhh......eeee.....ee...........hhhhh...hhhh.ee.hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhh..hhhhhhhhhhhhhhhhh................eeee......hhhhhh.eeeeee..eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qs8 B   6 DSKTLIHAGKLIDGKSDQVQSRISIVIDGNIISDIKKGFISSNDFEDYIDLRDHTVLPGLmDmHVHFGQEYQSKAQAPIKVEREmQAILATQHAYVTFKSGFTTVRQVGDSGLVAISLRDAINSGKLAGPRIFAAGKTIATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQFTQEEVDAVVSAAKDYGmWVAVHAHGAEGmKRAIKAGVDSIEHGTFmDLEAmDLmIENGTYYVPTISAGEFVAEKSKIDNFFPEIVRPKAASVGPQISDTFRKAYEKGVKIAFGTDAGVQKHGTNWKEFVYmVENGmPAmKAIQSATmETAKLLRIEDKLGSIESGKLADLIAVKGNPIEDISVLENVDVVIKDGLLY 410
                                    15        25        35        45        55        65| |     75        85    |   95       105       115       125       135       145       155       165       175       185       195       205       215       225    |  235      |245       255   |   265 |     275       285       295       305       315       325       335       345   |  |355    |  365       375       385       395       405     
                                                                                       66-MSE                  90-MSE                                                                                                                                     230-MSE     242-MSE          259-MSE|  |                                                                          344-MSE|  |     360-MSE                                              
                                                                                         68-MSE                                                                                                                                                                                             264-MSE                                                                              349-MSE                                                         
                                                                                                                                                                                                                                                                                               267-MSE                                                                              352-MSE
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QS8)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (K7N5L1_ALTMA | K7N5L1)
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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

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