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

(-) Description

Title :  CRYSTAL STRUCTURE OF PASTEURELLA MULTOCIDA N-ACETYL-D-NEURAMINIC ACID LYASE TRAPPED WITH PYRUVATE COVALENTLY BOUND THROUGH A SCHIFF BASE TO LYS164
 
Authors :  A. J. Fisher, N. Huynh
Date :  02 Jan 13  (Deposition) - 06 Nov 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Schiff Base, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Huynh, A. Aye, Y. Li, H. Yu, H. Cao, V. K. Tiwari, D. W. Shin, X. Chen, A. J. Fisher
Structural Basis For Substrate Specificity And Mechanism Of N-Acetyl-D-Neuraminic Acid Lyase From Pasteurella Multocida
Biochemistry V. 52 8570 2013
PubMed-ID: 24152047  |  Reference-DOI: 10.1021/BI4011754

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    Chains: A, B, C, D
    EC Number: 4.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NANA, PM1715
    Organism Scientific: PASTEURELLA MULTOCIDA SUBSP. GALLICIDA
    Organism Taxid: 1169409
    Strain: P1059
    Synonym: N-ACETYLNEURAMINATE PYRUVATE-LYASE, N-ACETYLNEURAMINIC ACID ALDOLASE, SIALATE LYASE, SIALIC ACID ALDOLASE, SIALIC ACID LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2KPI4Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:179 , TYR A:180 , PRO A:181 , ASN A:182 , HIS A:183BINDING SITE FOR RESIDUE PO4 A 301
02AC2SOFTWAREASN A:182 , HOH A:577 , HOH A:579BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREASP A:190 , GLU A:191 , HOH A:580 , HOH A:593BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREGLY A:226 , LEU A:228 , LYS A:229 , HOH A:581 , GLN B:224BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWARELYS A:2 , TYR A:132 , HOH A:522BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREALA B:179 , TYR B:180 , PRO B:181 , ASN B:182 , HIS B:183BINDING SITE FOR RESIDUE PO4 B 301
07AC7SOFTWAREASP B:190 , GLU B:191 , HOH B:568BINDING SITE FOR RESIDUE EDO B 302
08AC8SOFTWARELEU B:161 , ASN B:182 , HOH B:524 , HOH B:600BINDING SITE FOR RESIDUE EDO B 303
09AC9SOFTWARETYR C:180 , PRO C:181 , ASN C:182 , HIS C:183BINDING SITE FOR RESIDUE PO4 C 301
10BC1SOFTWARETHR C:107 , SER C:137 , ILE C:138 , PRO C:139 , THR C:142 , VAL C:144 , ILE C:146BINDING SITE FOR RESIDUE EDO C 302
11BC2SOFTWAREPHE C:189 , ASP C:190 , GLU C:191BINDING SITE FOR RESIDUE EDO C 303
12BC3SOFTWARETYR D:180 , PRO D:181 , ASN D:182 , HIS D:183BINDING SITE FOR RESIDUE PO4 D 301
13BC4SOFTWARETHR D:107 , TYR D:136 , SER D:137 , ILE D:138 , PRO D:139 , THR D:142 , VAL D:144 , ILE D:146BINDING SITE FOR RESIDUE EDO D 302
14BC5SOFTWAREASP D:190 , GLU D:191 , HOH D:565BINDING SITE FOR RESIDUE EDO D 303
15BC6SOFTWARELEU D:161 , ASN D:182BINDING SITE FOR RESIDUE EDO D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IMD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:270 -Pro A:271
2Glu B:270 -Pro B:271
3Glu C:270 -Pro C:271
4Glu D:270 -Pro D:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IMD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IMD)

(-) Exons   (0, 0)

(no "Exon" information available for 4IMD)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imda_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imd A   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVkFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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  
                                                                                                                                                                                            164-KPI                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imdb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imd B   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVkFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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  
                                                                                                                                                                                            164-KPI                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imdc_ C: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imd C   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVkFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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  
                                                                                                                                                                                            164-KPI                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imdd_ D: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imd D   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVkFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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  
                                                                                                                                                                                            164-KPI
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IMD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IMD)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KPI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:270 - Pro A:271   [ RasMol ]  
    Glu B:270 - Pro B:271   [ RasMol ]  
    Glu C:270 - Pro C:271   [ RasMol ]  
    Glu D:270 - Pro D:271   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4imd
    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
  NANA_PASMU | Q9CKB0
    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)
  4.1.3.3
    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
  NANA_PASMU | Q9CKB0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NANA_PASMU | Q9CKB0: 4imc 4ime 4imf 4img

(-) Related Entries Specified in the PDB File

4imc 4ime 4imf 4img