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(-) Description

Title :  CRYSTAL STRUCTURE OF A CREATININE AMIDOHYDROLASE (NPUN_F1913) FROM NOSTOC PUNCTIFORME PCC 73102 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Jun 10  (Deposition) - 25 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Creatinine Amidohydrolase (Npun_f1913) From Nostoc Punctiforme Pcc 73102 At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CREATININE AMIDOHYDROLASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NPUN_22DEC03_CONTIG1_REVISED_GENENPF1913, NPUN_F1913
    Organism Scientific: NOSTOC PUNCTIFORME PCC 73102
    Organism Taxid: 63737
    Synonym: CREATININASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric Unit (5, 35)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO16Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NI3Ligand/IonNICKEL (II) ION
5UNL3Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (3, 62)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO32Ligand/Ion1,2-ETHANEDIOL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4NI-1Ligand/IonNICKEL (II) ION
5UNL6Ligand/IonUNKNOWN LIGAND

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:31 , ASP A:40 , GLU A:172 , HOH A:531 , HOH A:532 , HOH A:645BINDING SITE FOR RESIDUE NI A 300
02AC2SOFTWAREASP A:91 , THR A:94 , HOH A:454 , HOH A:584 , HOH A:610 , LEU B:69 , HOH C:417BINDING SITE FOR RESIDUE EDO A 401
03AC3SOFTWAREGLN A:142 , ARG A:198 , TYR A:200 , PHE A:244 , HOH A:474BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWARELEU A:69 , HOH A:509 , HOH A:562 , HOH A:585 , THR B:94 , CYS B:95 , HOH B:665 , HOH B:733BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREHIS B:31 , ASP B:40 , GLU B:172 , HOH B:736 , HOH B:739 , HOH B:742BINDING SITE FOR RESIDUE NI B 300
06AC6SOFTWAREHOH A:620 , GLY B:0 , MSE B:1 , ALA B:49 , GLY B:52 , ASP B:53BINDING SITE FOR RESIDUE EDO B 402
07AC7SOFTWAREALA B:144 , ASN B:145BINDING SITE FOR RESIDUE EDO B 405
08AC8SOFTWAREASP A:130 , LEU A:131 , ASP B:130 , LEU B:131 , GLN B:132 , ASP C:130 , GLN C:132BINDING SITE FOR RESIDUE EDO B 406
09AC9SOFTWAREGLN B:142 , VAL B:143BINDING SITE FOR RESIDUE EDO B 408
10BC1SOFTWAREGLN B:16 , LYS B:19 , ALA B:99 , GLY B:100 , HOH B:756 , HOH B:798BINDING SITE FOR RESIDUE EDO B 409
11BC2SOFTWAREGLN B:142 , GLU B:243 , PHE B:244 , HOH B:808 , ARG C:198 , TYR C:200BINDING SITE FOR RESIDUE EDO B 410
12BC3SOFTWARELYS B:235 , HOH B:591 , SER C:190 , PRO C:191BINDING SITE FOR RESIDUE EDO B 411
13BC4SOFTWAREGLN A:132 , HOH A:445 , LEU B:131 , GLN B:132 , HOH B:788BINDING SITE FOR RESIDUE EDO B 412
14BC5SOFTWAREHIS C:31 , ASP C:40 , GLU C:172 , HOH C:909 , HOH C:911 , HOH C:913BINDING SITE FOR RESIDUE NI C 300
15BC6SOFTWAREHOH B:677 , HOH B:818 , LEU C:69 , ASP C:91 , THR C:94 , HOH C:777 , HOH C:843 , HOH C:901BINDING SITE FOR RESIDUE EDO C 407
16BC7SOFTWARELYS C:118 , GLN C:142 , VAL C:143 , HOH C:866 , HOH C:961 , HOH C:965BINDING SITE FOR RESIDUE EDO C 413
17BC8SOFTWARETHR C:72 , ALA C:73 , PRO C:75 , LYS C:98 , ALA C:99 , HOH C:941 , HOH C:989BINDING SITE FOR RESIDUE EDO C 414
18BC9SOFTWAREGLY C:0 , ALA C:49 , GLY C:52 , ASP C:53 , VAL C:59BINDING SITE FOR RESIDUE EDO C 415
19CC1SOFTWAREALA C:144 , ASN C:145 , HOH C:976BINDING SITE FOR RESIDUE EDO C 416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NO4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NO4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NO4)

(-) Exons   (0, 0)

(no "Exon" information available for 3NO4)

(-) 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:264
 aligned with B2J3U5_NOSP7 | B2J3U5 from UniProtKB/TrEMBL  Length:248

    Alignment length:264
                                            1                                                                                                                                                                                                                                                       
                                     -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    
         B2J3U5_NOSP7     - ----------------MLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGMALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFMCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRMGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhh..ee.hhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhh.ee........hhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3no4 A -15 DKIHHHHHHENLYFQGmLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGmALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFmCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRmGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
                                    -6      |  4        14        24        34        44        54        64  |     74        84        94       104       114       124       134       144   |   154       164       174       184       194       204       214       224       234       244    
                                            1-MSE                                                            67-MSE                                                                          148-MSE                                                           214-MSE                              


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with B2J3U5_NOSP7 | B2J3U5 from UniProtKB/TrEMBL  Length:248

    Alignment length:256
                                    1                                                                                                                                                                                                                                                       
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
         B2J3U5_NOSP7     - --------MLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGMALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFMCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRMGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhh.ee........hhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no4 B  -7 HENLYFQGmLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGmALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFmCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRmGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
                                    |2        12        22        32        42        52        62    |   72        82        92       102       112       122       132       142     | 152       162       172       182       192       202       212 |     222       232       242      
                                    1-MSE                                                            67-MSE                                                                          148-MSE                                                           214-MSE                              


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with B2J3U5_NOSP7 | B2J3U5 from UniProtKB/TrEMBL  Length:248

    Alignment length:250
                              1                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
         B2J3U5_NOSP7     - --MLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGMALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFMCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRMGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Creatininase-3no4C01 C:3-241                                                                                                                                                                                                                   ------- Pfam domains (1)
           Pfam domains (2) ----Creatininase-3no4C02 C:3-241                                                                                                                                                                                                                   ------- Pfam domains (2)
           Pfam domains (3) ----Creatininase-3no4C03 C:3-241                                                                                                                                                                                                                   ------- Pfam domains (3)
         Sec.struct. author ..ee.hhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhh.ee........hhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no4 C  -1 QGmLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATGAIVGPTINVGmALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAGFSKFYFINGHGGNIATLKAAFSETYAHLEDLQIANAQQVQCQVANWFmCGSVYKLAKELYGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYSAADFRVRYPDGRmGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD 248
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     | 218       228       238       248
                              1-MSE                                                            67-MSE                                                                          148-MSE                                                           214-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  (0, 0)

(no "SCOP Domain" information available for 3NO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NO4)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Creatininase] (2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3NO4)

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