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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPERTHERMOPHILIC NITRILASE
 
Authors :  J. Raczynska, C. Vorgias, G. Antranikian, W. Rypniewski
Date :  07 Nov 09  (Deposition) - 24 Nov 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Sandwich, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Raczynska, C. E. Vorgias, G. Antranikian, W. Rypniewski
Crystallographic Analysis Of A Thermoactive Nitrilase.
J. Struct. Biol. V. 173 294 2010
PubMed-ID: 21095228  |  Reference-DOI: 10.1016/J.JSB.2010.11.017

(-) Compounds

Molecule 1 - BETA UREIDOPROPIONASE (BETA-ALANINE SYNTHASE)
    Chains: A, B
    EC Number: 3.5.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NIT-30, PAB1449, PYRAB13990
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 272844
    Strain: GE5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2BR13Ligand/IonBROMIDE ION
3CSX2Mod. Amino AcidS-OXY CYSTEINE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:107 , GLY A:109 , LYS A:110 , ARG A:132BINDING SITE FOR RESIDUE BR A 263
02AC2SOFTWAREGLU A:15 , PRO A:16 , ASP A:17 , LYS A:18BINDING SITE FOR RESIDUE BR A 264
03AC3SOFTWAREGLY A:103 , ARG A:105BINDING SITE FOR RESIDUE BR A 265
04AC4SOFTWARELYS A:3 , GLY A:34 , GLY B:34BINDING SITE FOR RESIDUE BR A 266
05AC5SOFTWAREARG A:132 , VAL A:133BINDING SITE FOR RESIDUE BR A 267
06AC6SOFTWAREGLU A:153 , GLU B:153 , PHE B:261BINDING SITE FOR RESIDUE BR A 268
07AC7SOFTWARECSX A:146 , TRP A:149 , LEU A:172 , VAL A:173 , MET A:174 , BR A:270 , HOH A:306 , HOH A:322BINDING SITE FOR RESIDUE ACY A 269
08AC8SOFTWARETRP A:149 , LEU A:172 , ACY A:269 , HOH A:306 , HOH A:322BINDING SITE FOR RESIDUE BR A 270
09AC9SOFTWAREGLY B:103 , PRO B:104 , ARG B:105BINDING SITE FOR RESIDUE BR B 263
10BC1SOFTWARELYS B:110 , ARG B:132BINDING SITE FOR RESIDUE BR B 264
11BC2SOFTWARELYS B:22BINDING SITE FOR RESIDUE BR B 265
12BC3SOFTWAREPRO B:175BINDING SITE FOR RESIDUE BR B 266
13BC4SOFTWAREALA B:233 , GLU B:234BINDING SITE FOR RESIDUE BR B 267
14BC5SOFTWARETRP B:149 , LEU B:172 , VAL B:173 , MET B:174 , BR B:269 , HOH B:307 , HOH B:341BINDING SITE FOR RESIDUE ACY B 268
15BC6SOFTWARETRP B:149 , LEU B:172 , ACY B:268BINDING SITE FOR RESIDUE BR B 269
16BC7SOFTWAREARG B:255 , GLU B:257 , HOH B:286 , HOH B:296 , HOH B:340 , HOH B:359BINDING SITE FOR RESIDUE MG B 270

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:63 -Pro A:64
2Ile B:63 -Pro B:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.NITR_PYRAB2-237
 		  2A:2-237
B:2-237

(-) Exons   (0, 0)

(no "Exon" information available for 3KLC)

(-) 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:261
 aligned with NITR_PYRAB | Q9UYV8 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                    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 
           NITR_PYRAB     2 VKVAYVQMNPQILEPDKNYSKAEKLIKEASKQGAQLVVLPELFDTGYNFETREEVFEIAQKIPEGETTTFLMDVARDTGVYIVAGTAEKDGDVLYNSAVVVGPRGFIGKYRKIHLFYREKFFFEPGDLGFRVFDLGFMKVGVMICFDWFFPESARTLALKGADVIAHPANLVMPYAPRAMPIRALENKVYTVTADRVGEERGLKFIGKSLIASPKAEVLSMASETEEEVGVAEIDLYLVRNKRINDLNDIFKDRREEYYFR 262
               SCOP domains d3klca_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhhh...eee............hhhhhhh.......hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeeee...ee..ee.....eee.....eeee......eeeeee.hhhhhhh.eee..eehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CN_HYDROLASE  PDB: A:2-237 UniProt: 2-237                                                                                                                                                                                                   ------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3klc A   2 VKVAYVQMNPQILEPDKNYSKAEKLIKEASKQGAQLVVLPELFDTGYNFETREEVFEIAQKIPEGETTTFLMDVARDTGVYIVAGTAEKDGDVLYNSAVVVGPRGFIGKYRKIHLFYREKFFFEPGDLGFRVFDLGFMKVGVMIcFDWFFPESARTLALKGADVIAHPANLVMPYAPRAMPIRALENKVYTVTADRVGEERGLKFIGKSLIASPKAEVLSMASETEEEVGVAEIDLSLVRNKRINDLNDIFKDRREEYYFR 262
                                    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 
                                                                                                                                                                          146-CSX                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with NITR_PYRAB | Q9UYV8 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                    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 
           NITR_PYRAB     2 VKVAYVQMNPQILEPDKNYSKAEKLIKEASKQGAQLVVLPELFDTGYNFETREEVFEIAQKIPEGETTTFLMDVARDTGVYIVAGTAEKDGDVLYNSAVVVGPRGFIGKYRKIHLFYREKFFFEPGDLGFRVFDLGFMKVGVMICFDWFFPESARTLALKGADVIAHPANLVMPYAPRAMPIRALENKVYTVTADRVGEERGLKFIGKSLIASPKAEVLSMASETEEEVGVAEIDLYLVRNKRINDLNDIFKDRREEYYFR 262
               SCOP domains d3klcb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhhh.eeeee............hhhhhhhhhee...hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeeee...ee..ee.....eee.....eeee......eeeeee.hhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CN_HYDROLASE  PDB: B:2-237 UniProt: 2-237                                                                                                                                                                                                   ------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3klc B   2 VKVAYVQMNPQILEPDKNYSKAEKLIKEASKQGAQLVVLPELFDTGYNFETREEVFEIAQKIPEGETTTFLMDVARDTGVYIVAGTAEKDGDVLYNSAVVVGPRGFIGKYRKIHLFYREKFFFEPGDLGFRVFDLGFMKVGVMIcFDWFFPESARTLALKGADVIAHPANLVMPYAPRAMPIRALENKVYTVTADRVGEERGLKFIGKSLIASPKAEVLSMASETEEEVGVAEIDLSLVRNKRINDLNDIFKDRREEYYFR 262
                                    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 
                                                                                                                                                                          146-CSX
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KLC)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NITR_PYRAB | Q9UYV8)
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:0000257    nitrilase activity    Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH3. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides.
biological process
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NITR_PYRAB | Q9UYV8: 3ivz 3iw3 3ki8

(-) Related Entries Specified in the PDB File

3ivz UNLIGANDED NITRILASE - TETRAGONAL FORM
3iw3 NITRILASE WITH ACETATE ION - TETRAGONAL FORM
3ki8 NITRILASE WITH ACETATE ION - MONOCLINIC FORM