2B4Y - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN SIRTUIN HOMOLOG 5

Authors :   J. R. Min, T. Antoshenko, A. Dong, A. Schuetz, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   27 Sep 05 (Deposition) - 28 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Histone Deacetylase, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Antoshenko, J. R. Min, A. Schuetz, P. Loppnau, A. M. Edwards, C. H. Arrowsmith, A. Bochkarev, A. N. Plotnikov
Crystal Structure Of Human Sirtuin Homolog 5 In Complex With Nad
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - NAD-DEPENDENT DEACETYLASE SIRTUIN-5
	Chains	:	A, B, C, D
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SIRT5, SIR2L5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SIR2-LIKE PROTEIN 5

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

No.	Name	Count	Type	Full Name
1	APR	4	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EPE	4	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (3, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:166 , CYS A:169 , CYS A:207 , CYS A:212	BINDING SITE FOR RESIDUE ZN A 1001
02	AC2	SOFTWARE	CYS B:166 , CYS B:169 , CYS B:207 , CYS B:212	BINDING SITE FOR RESIDUE ZN B 2001
03	AC3	SOFTWARE	CYS C:166 , CYS C:169 , CYS C:207 , CYS C:212	BINDING SITE FOR RESIDUE ZN C 3001
04	AC4	SOFTWARE	CYS D:166 , CYS D:169 , CYS D:207 , CYS D:212	BINDING SITE FOR RESIDUE ZN D 4001
05	AC5	SOFTWARE	GLY A:58 , ALA A:59 , GLY A:60 , ALA A:63 , GLU A:64 , GLN A:140 , HIS A:158 , GLY A:249 , THR A:250 , SER A:251 , ASN A:275 , THR A:276 , GLU A:277 , PRO A:292 , CYS A:293 , EPE A:1003 , HOH A:1033 , HOH A:1070 , HOH A:1160 , HOH A:1176 , HOH A:1190	BINDING SITE FOR RESIDUE APR A 1002
06	AC6	SOFTWARE	GLY B:58 , ALA B:59 , GLY B:60 , GLU B:64 , THR B:69 , GLN B:140 , HIS B:158 , GLY B:249 , THR B:250 , SER B:251 , ASN B:275 , THR B:276 , GLU B:277 , CYS B:293 , EPE B:2003 , HOH B:2028 , HOH B:2031 , HOH B:2160 , HOH B:2171	BINDING SITE FOR RESIDUE APR B 2002
07	AC7	SOFTWARE	HOH B:2043 , GLY C:58 , ALA C:59 , GLY C:60 , ALA C:63 , GLU C:64 , THR C:69 , PHE C:70 , ARG C:71 , GLN C:140 , HIS C:158 , GLY C:249 , THR C:250 , SER C:251 , VAL C:254 , ASN C:275 , THR C:276 , GLU C:277 , PRO C:292 , CYS C:293 , EPE C:3003 , HOH C:3005 , HOH C:3067 , HOH C:3082 , HOH C:3145	BINDING SITE FOR RESIDUE APR C 3002
08	AC8	SOFTWARE	GLY D:58 , ALA D:59 , GLY D:60 , GLU D:64 , THR D:69 , PHE D:70 , GLN D:140 , HIS D:158 , GLY D:249 , THR D:250 , SER D:251 , VAL D:254 , ASN D:275 , THR D:276 , GLU D:277 , PRO D:292 , CYS D:293 , EPE D:4003 , HOH D:4007 , HOH D:4039 , HOH D:4072 , HOH D:4128 , HOH D:4135	BINDING SITE FOR RESIDUE APR D 4002
09	AC9	SOFTWARE	ALA A:82 , ALA A:86 , TYR A:102 , ARG A:105 , HIS A:158 , VAL A:221 , TRP A:222 , PHE A:223 , GLY A:224 , GLU A:225 , APR A:1002 , HOH A:1186	BINDING SITE FOR RESIDUE EPE A 1003
10	BC1	SOFTWARE	ALA B:82 , ALA B:86 , TYR B:102 , ARG B:105 , VAL B:221 , TRP B:222 , PHE B:223 , APR B:2002	BINDING SITE FOR RESIDUE EPE B 2003
11	BC2	SOFTWARE	PHE C:70 , ALA C:82 , ALA C:86 , ARG C:105 , HIS C:158 , VAL C:221 , PHE C:223 , GLU C:225 , LEU C:227 , APR C:3002 , HOH C:3144 , HOH C:3147 , SER D:168 , CYS D:169	BINDING SITE FOR RESIDUE EPE C 3003
12	BC3	SOFTWARE	SER C:168 , CYS C:169 , PHE D:70 , ALA D:82 , ALA D:86 , ARG D:105 , HIS D:158 , VAL D:221 , PHE D:223 , GLU D:225 , LEU D:227 , TYR D:255 , APR D:4002 , HOH D:4125 , HOH D:4149	BINDING SITE FOR RESIDUE EPE D 4003

(no "SS Bond" information available for 2B4Y)

Asymmetric Unit

No.	Residues
1	Ser A:178	-	Pro A:179
2	Tyr A:255	-	Pro A:256
3	Ser B:178	-	Pro B:179
4	Tyr B:255	-	Pro B:256
5	Ser C:178	-	Pro C:179
6	Tyr C:255	-	Pro C:256
7	Ser D:178	-	Pro D:179
8	Tyr D:255	-	Pro D:256

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029042	F	285	L	SIR5_HUMAN	Polymorphism	9464003	A/B/C/D	F	285	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029042	F	285	L	SIR5_HUMAN	Polymorphism	9464003	A	F	285	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029042	F	285	L	SIR5_HUMAN	Polymorphism	9464003	B	F	285	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029042	F	285	L	SIR5_HUMAN	Polymorphism	9464003	C	F	285	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029042	F	285	L	SIR5_HUMAN	Polymorphism	9464003	D	F	285	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR5_HUMAN	41-309	4	A:41-302 B:41-302 C:41-302 D:41-302

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR5_HUMAN	41-309	1	A:41-302 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR5_HUMAN	41-309	1	- B:41-302 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR5_HUMAN	41-309	1	- - C:41-302 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR5_HUMAN	41-309	1	- - - D:41-302

(no "Exon" information available for 2B4Y)

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:260
 aligned with SIR5_HUMAN | Q9NXA8 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    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       
           SIR5_HUMAN    36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
               SCOP domains d2b4ya1 A:36-302 NAD-dependent d       eacetylase sirtuin-5                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhhhh.-------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------- SAPs(SNPs)
                    PROSITE -----SIRTUIN  PDB: A:41-302 UniProt: 41-309                                                                                                                                                                                                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4y A  36 PSSSmADFRKFFAKAKHIVIISGAGVSAESGV-------GYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVmGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAmFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 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       
                                |                         67      75                               109-MSE                                                                                                                                               259-MSE                                       
                               40-MSE

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with SIR5_HUMAN | Q9NXA8 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    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       
           SIR5_HUMAN    36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
               SCOP domains d2b4yb_ B: NAD-dependent deacetyla     se sirtuin-5                                                                                                                                                                                                                         SCOP domains
               CATH domains 2b4yB01 TPP-binding domain     -----------------------------------------------2b4yB01 B:36-66,B:114-158,B:227-302          --------------------------------------------------------------------2b4yB01 B:36-66,B:114-158,B:227-302 TPP-binding domain                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhhhh...-----......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeee....hhhhhh....eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------- SAPs(SNPs)
                    PROSITE -----SIRTUIN  PDB: B:41-302 UniProt: 41-309                                                                                                                                                                                                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4y B  36 PSSSmADFRKFFAKAKHIVIISGAGVSAESGVPT-----GYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVmGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAmFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 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       
                               40-MSE                       69    75                               109-MSE                                                                                                                                               259-MSE

Chain C from PDB  Type:PROTEIN  Length:263
 aligned with SIR5_HUMAN | Q9NXA8 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    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       
           SIR5_HUMAN    36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
               SCOP domains d2b4yc_ C: NAD-dependent deacetylase     sirtuin-5                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhhhh.....----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh....eeeee.....hhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------- SAPs(SNPs)
                    PROSITE -----SIRTUIN  PDB: C:41-302 UniProt: 41-309                                                                                                                                                                                                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4y C  36 PSSSmADFRKFFAKAKHIVIISGAGVSAESGVPTFR----YWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVmGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAmFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                |   45        55        65     |   -|       85        95       105   |   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   |   265       275       285       295       
                               40-MSE                         71   76                              109-MSE                                                                                                                                               259-MSE

Chain D from PDB  Type:PROTEIN  Length:262
 aligned with SIR5_HUMAN | Q9NXA8 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:267
                                    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       
           SIR5_HUMAN    36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
               SCOP domains d2b4yd_ D: NAD-dependent deacetylas     e sirtuin-5                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhhhh....-----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......eeeeee....hhhhhh....eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------- SAPs(SNPs)
                    PROSITE -----SIRTUIN  PDB: D:41-302 UniProt: 41-309                                                                                                                                                                                                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4y D  36 PSSSmADFRKFFAKAKHIVIISGAGVSAESGVPTF-----YWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVmGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAmFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                |   45        55        65    |    -|       85        95       105   |   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   |   265       275       285       295       
                               40-MSE                        70    76                              109-MSE                                                                                                                                               259-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: Sir2 family of transcriptional regulators (31)

Protein domain: NAD-dependent deacetylase sirtuin-5 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2b4ya1	A:36-302
1b	d2b4yb_	B:
1c	d2b4yc_	C:
1d	d2b4yd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Human (Homo sapiens) (9)

2b4yB01

B:36-66,B:114-158,B:227-302

(no "Pfam Domain" information available for 2B4Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SIR5_HUMAN | Q9NXA8)

molecular function
	GO:0003950	NAD+ ADP-ribosyltransferase activity	Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0061697	protein-glutaryllysine deglutarylase activity	Catalysis of the reaction: protein-glutaryllysine + H2O => protein-lysine + glutarate. This reaction is the removal of a glutaryl group from a glutarylated lysine residue of a protein or peptide.
	GO:0036054	protein-malonyllysine demalonylase activity	Catalysis of the reaction: protein-malonyllysine + H2O => protein-lysine + malonate. This reaction is the removal of a malonyl group (CO-CH2-CO) from a malonylated lysine residue of a protein or peptide.
	GO:0036055	protein-succinyllysine desuccinylase activity	Catalysis of the reaction: protein-succinyllysine + H2O => protein-lysine + succinate. This reaction is the removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue of a protein or peptide.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
	GO:0010667	negative regulation of cardiac muscle cell apoptotic process	Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
	GO:2000378	negative regulation of reactive oxygen species metabolic process	Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process.
	GO:0061699	peptidyl-lysine deglutarylation	The removal of a glutaryl group (CO-CH2-CH2--CH2-CO) from a glutarylated lysine residue in a peptide or protein.
	GO:0036047	peptidyl-lysine demalonylation	The process of removing a malonyl group (CO-CH2-CO) from an malonylated lysine residue in a peptide or protein.
	GO:0036049	peptidyl-lysine desuccinylation	The removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue in a peptide or protein.
	GO:0006471	protein ADP-ribosylation	The transfer, from NAD, of ADP-ribose to protein amino acids.
	GO:0006476	protein deacetylation	The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
	GO:0061698	protein deglutarylation	The removal of a glutaryl group (CO-CH2-CH2-CH2-CO) from a residue in a peptide or protein.
	GO:0036046	protein demalonylation	The removal of a malonyl group (CO-CH2-CO), from an amino acid residue within a protein or peptide.
	GO:0036048	protein desuccinylation	The removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein.
	GO:0010566	regulation of ketone biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	2b4y
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(no "Related Entries Specified in the PDB File" available for 2B4Y)

Description

Compounds

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Ligands, Modified Residues, Ions (4, 24)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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