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(-) Description

Title :  THE BICYCLIC INTERMEDIATE STRUCTURE PROVIDES INSIGHTS INTO THE DESUCCINYLATION MECHANISM OF SIRT5
 
Authors :  Y. Zhou, Q. Hao
Date :  11 May 12  (Deposition) - 20 Jun 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Zn-Binding Domain, Rossmann Fold Domain, Nad-Dependent Demalonylase And Desuccinylase, Mitochondrial Sirtuin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhou, H. Zhang, B. He, J. Du, H. Lin, R. A. Cerione, Q. Hao
The Bicyclic Intermediate Structure Provides Insights Into The Desuccinylation Mechanism Of Human Sirtuin 5 (Sirt5)
J. Biol. Chem. V. 287 28307 2012
PubMed-ID: 22767592  |  Reference-DOI: 10.1074/JBC.M112.384511

(-) Compounds

Molecule 1 - NAD-DEPENDENT LYSINE DEMALONYLASE AND DESUCCINYLASE SIRTUIN-5, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-F1
    Expression System Strain: BL21 R2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUE 34-302
    Gene: SIR2L5, SIRT5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SIR2-LIKE PROTEIN 5
 
Molecule 2 - PEPTIDE FROM HISTONE H3.1
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUE 5-16
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, HISTONE H3/L
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CGK2Ligand/Ion3-[(2R,3AR,5R,6R,6AR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-2,6-DIHYDROXYTETRAHYDROFURO[2,3-D][1,3]OXATHIOL-2-YL]PROPANOIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CGK1Ligand/Ion3-[(2R,3AR,5R,6R,6AR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-2,6-DIHYDROXYTETRAHYDROFURO[2,3-D][1,3]OXATHIOL-2-YL]PROPANOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CGK1Ligand/Ion3-[(2R,3AR,5R,6R,6AR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-2,6-DIHYDROXYTETRAHYDROFURO[2,3-D][1,3]OXATHIOL-2-YL]PROPANOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:166 , CYS A:169 , CYS A:207 , CYS A:212BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS B:166 , CYS B:169 , CYS B:207 , CYS B:212BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREGLY A:58 , ALA A:59 , GLY A:60 , ALA A:63 , GLU A:64 , THR A:69 , PHE A:70 , ARG A:71 , TYR A:102 , ARG A:105 , GLN A:140 , ILE A:142 , HIS A:158 , VAL A:220 , PHE A:223 , GLY A:249 , THR A:250 , SER A:251 , VAL A:254 , ASN A:275 , THR A:276 , GLU A:277 , PRO A:292 , CYS A:293 , HOH A:511 , HOH A:697 , LYS C:9 , HOH C:201 , HOH C:202 , HOH C:203BINDING SITE FOR RESIDUE CGK C 101
4AC4SOFTWAREGLY B:58 , ALA B:59 , GLY B:60 , ALA B:63 , GLU B:64 , THR B:69 , PHE B:70 , ARG B:71 , TYR B:102 , ARG B:105 , GLN B:140 , ILE B:142 , HIS B:158 , VAL B:220 , PHE B:223 , GLY B:249 , THR B:250 , SER B:251 , VAL B:254 , ASN B:275 , THR B:276 , GLU B:277 , PRO B:292 , CYS B:293 , HOH B:596 , HOH B:698 , LYS D:9 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:205 , HOH D:206BINDING SITE FOR RESIDUE CGK D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F56)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ala A:73 -Gly A:74
2Ser A:178 -Pro A:179
3Tyr A:255 -Pro A:256
4Ser B:178 -Pro B:179
5Tyr B:255 -Pro B:256
6Thr C:11 -Gly C:12
7Thr D:11 -Gly D:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F56)

(-) Exons   (0, 0)

(no "Exon" information available for 4F56)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f56 A  36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                    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       


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.eeeeee.hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f56 B  31 SFTARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4f56 C   6 TARKSTG  12


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4f56 D   6 TARKSTG  12
   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 4F56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F56)

(-) Gene Ontology  (55, 56)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        SIR5_HUMAN | Q9NXA8: 2b4y 2nyr 3rig 3riy 4f4u 4g1c 4hda 5bwl

(-) Related Entries Specified in the PDB File

3rig 3riy 4f4u