Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF SUCCINYLGLUTAMATE DESUCCINALASE FROM VIBRIO PARAHAEMOLYTICUS (RIMD 2210633) AT THE RESOLUTION 2.3 A, NORTHEAST STRUCTURAL GENOMICS TARGET VPR14
 
Authors :  A. P. Kuzin, M. Abashidze, F. Forouhar, J. Benach, W. Zhou, T. Acton, Northeast Structural Genomics Consortium (Nesg)
Date :  19 Oct 05  (Deposition) - 25 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nesg, Vpr14, X-Ray Structure, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, M. Abashidze, F. Forouhar, J. Benach, W. Zhou, T. Acton, R. Xiao, K. Conover, L. C. Ma, R. Kellie, K. E. Cunningham, G. T. Montelione, L. Tong, J. F. Hunt
X-Ray Structure Of Succinylglutamate Desuccinalase From Vibrio Parahaemolyticus (Rimd 2210633) At The Resolution 2. 3 A, Northeast Structural Genomics Target Vpr14
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINYLGLUTAMATE DESUCCINYLASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3) + MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ASTE
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:63 , GLU A:66 , HIS A:155 , HOH A:584BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS B:63 , GLU B:66 , HIS B:155 , HOH B:551BINDING SITE FOR RESIDUE ZN B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BCO)

(-) 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:338
 aligned with ASTE_VIBPA | Q87Q40 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:339
                                    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         
           ASTE_VIBPA     4 SLFRQSFLTDTLDVHIDVAPAEQVLSNGVQLKLYQRGVLEVIPENPTQETKNIIISCGIHGDETAPMELVDSIIKDIESGFQKVDARCLFIIAHPESTLAHTRFLEENLNRLFDEKEHEPTKELAIADTLKLLVRDFYQDTEPKTRWHLDLHCAIRGSKHYTFAVSPKTRHPVRSKALVDFLDSAHIEAVLLSNSPSSTFSWYSAENYSAQALTMELGRVARIGENALDRLTAFDLALRNLIAEAQPEHLSKPCIKYRVSRTIVRLHDDFDFMFDDNVENFTSFVHGEVFGHDGDKPLMAKNDNEAIVFPNRHVAIGQRAALMVCEVKTRFEEGELVYD 342
               SCOP domains d2bcoa1 A:4-342  Succinylglutamate desuccinylase AstE                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...-...eeee.....eeeeee..eeeee.........eeeeee......hhhhhhhhhhhhhhhh.......eeeeee.hhhhhhh.......hhhhh........hhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee.......eeeee........hhhhhhhhhhhh..eeee......hhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhhhhh...........eeeeeeeeee.....eee.........ee.....eeeee..eeee......eee..........eeeeeeee..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bco A   4 SLFRQSFLTDTLDVHI-VAPAEQVLSNGVQLKLYQRGVLEVIPENPTQETKNIIISCGIHGDETAPmELVDSIIKDIESGFQKVDARCLFIIAHPESTLAHTRFLEENLNRLFDEKEHEPTKELAIADTLKLLVRDFYQDTEPKTRWHLDLHCAIRGSKHYTFAVSPKTRHPVRSKALVDFLDSAHIEAVLLSNSPSSTFSWYSAENYSAQALTmELGRVARIGENALDRLTAFDLALRNLIAEAQPEHLSKPCIKYRVSRTIVRLHDDFDFmFDDNVENFTSFVHGEVFGHDGDKPLmAKNDNEAIVFPNRHVAIGQRAALmVCEVKTRFEEGELVYD 342
                                    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         
                                          19 |                                               70-MSE                                                                                                                                             218-MSE                                                   276-MSE                   302-MSE                 326-MSE            
                                            21                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with ASTE_VIBPA | Q87Q40 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:339
                                    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         
           ASTE_VIBPA     4 SLFRQSFLTDTLDVHIDVAPAEQVLSNGVQLKLYQRGVLEVIPENPTQETKNIIISCGIHGDETAPMELVDSIIKDIESGFQKVDARCLFIIAHPESTLAHTRFLEENLNRLFDEKEHEPTKELAIADTLKLLVRDFYQDTEPKTRWHLDLHCAIRGSKHYTFAVSPKTRHPVRSKALVDFLDSAHIEAVLLSNSPSSTFSWYSAENYSAQALTMELGRVARIGENALDRLTAFDLALRNLIAEAQPEHLSKPCIKYRVSRTIVRLHDDFDFMFDDNVENFTSFVHGEVFGHDGDKPLMAKNDNEAIVFPNRHVAIGQRAALMVCEVKTRFEEGELVYD 342
               SCOP domains d2bcob_ B: Succi nylglutamate desuccinylase AstE                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....-...eeee.....eeeeee..eeeee.........eeeeee......hhhhhhhhhhhhhhhhh......eeeeee.hhhhhhh.......hhhhh........hhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee.......eeeee........hhhhhhhhhhh...eeee......hhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhhhhh.-----.....eee.....----------.........------------------------.........-------.........ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bco B   4 SLFRQSFLTDTLDVHI-VAPAEQVLSNGVQLKLYQRGVLEVIPENPTQETKNIIISCGIHGDETAPmELVDSIIKDIESGFQKVDARCLFIIAHPESTLAHTRFLEENLNRLFDEKEHEPTKELAIADTLKLLVRDFYQDTEPKTRWHLDLHCAIRGSKHYTFAVSPKTRHPVRSKALVDFLDSAHIEAVLLSNSPSSTFSWYSAENYSAQALTmELGRVARIGENALDRLTAFDLALRNLIAE-----LSKPCIKYRVSRT----------mFDDNVENF------------------------AIVFPNRHV-------LmVCEVKTRFEEGELVYD 342
                                    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 |       -  |    283|        -         -     | 313   |     - ||    333         
                                          19 |                                               70-MSE                                                                                                                                             218-MSE                      247   253         265        276-MSE 284                      309     317     325|                
                                            21                                                                                                                                                                                                                                                                                                              326-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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BCO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ASTE_VIBPA | Q87Q40)
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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0009017    succinylglutamate desuccinylase activity    Catalysis of the reaction: N-succinyl-L-glutamate + H(2)O = L-glutamate + succinate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019544    arginine catabolic process to glutamate    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including glutamate.
    GO:0019545    arginine catabolic process to succinate    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including succinate.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bco)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bco
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ASTE_VIBPA | Q87Q40
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ASTE_VIBPA | Q87Q40
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2BCO)

(-) Related Entries Specified in the PDB File

1yw4
1yw6 RELATED ID: VPR14 RELATED DB: TARGETDB