Q9NZC9 (SMAL1_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 29, 2013.
Version 106.
History...
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 EC=3.6.4.- Alternative name(s): HepA-related protein Short name=hHARP Sucrose nonfermenting protein 2-like 1 | ||||
| Gene names |
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| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 954 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | ATP-dependent annealing helicase that catalyzes the rewinding of the stably unwound DNA. Rewinds single-stranded DNA bubbles that are stably bound by replication protein A (RPA). Acts throughout the genome to reanneal stably unwound DNA, performing the opposite reaction of many enzymes, such as helicases and polymerases, that unwind DNA. Ref.12 |
| Subcellular location | Nucleus By similarity. |
| Tissue specificity | Ubiquitously expressed, with high levels in testis. Ref.1 Ref.2 |
| Involvement in disease | Schimke immuno-osseous dysplasia (SIOD) [MIM:242900]: Causes spondyloepiphyseal dysplasia, renal dysfunction and T-cell immunodeficiency. Approximately half of all patients also exhibit hyperthyroidism, while around half also exhibit episodal cerebral ischema. |
| Sequence similarities | Belongs to the SNF2/RAD54 helicase family. SMARCAL1 subfamily. Contains 2 HARP domains. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. |
| Sequence caution | The sequence BAA90955.1 differs from that shown. Reason: Erroneous initiation. |
Ontologies
| Keywords | |
|---|---|
| Cellular component | Nucleus |
| Coding sequence diversity | Polymorphism |
| Disease | Disease mutation |
| Domain | Coiled coil Repeat |
| Ligand | ATP-binding Nucleotide-binding |
| Molecular function | Helicase Hydrolase |
| PTM | Phosphoprotein |
| Technical term | Complete proteome Reference proteome |
| Gene Ontology (GO) | |
| Biological_process | chromatin modification Inferred from electronic annotation. Source: InterPro regulation of transcription from RNA polymerase II promoterInferred from mutant phenotype Ref.12. Source: UniProtKB |
| Cellular_component | nucleus Inferred from direct assay Ref.12. Source: UniProtKB |
| Molecular_function | ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA bindingInferred from electronic annotation. Source: InterPro DNA-dependent ATPase activityInferred from mutant phenotype Ref.12. Source: UniProtKB annealing helicase activityInferred from direct assay PubMed 22705370. Source: UniProtKB helicase activityInferred from electronic annotation. Source: UniProtKB-KW |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 954 | 954 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 | PRO_0000074348 | |||||
Regions | |||||||||
| Domain | 226 – 303 | 78 | HARP 1 | ||||||
| Domain | 327 – 398 | 72 | HARP 2 | ||||||
| Domain | 445 – 600 | 156 | Helicase ATP-binding | ||||||
| Domain | 716 – 869 | 154 | Helicase C-terminal | ||||||
| Nucleotide binding | 458 – 465 | 8 | ATP By similarity | ||||||
| Coiled coil | 3 – 34 | 32 | Potential | ||||||
| Motif | 549 – 552 | 4 | DESH box | ||||||
Amino acid modifications | |||||||||
| Modified residue | 151 | 1 | Phosphoserine Ref.9 | ||||||
Natural variations | |||||||||
| Natural variant | 22 | 1 | A → G. Ref.5 Corresponds to variant rs17851400 [ dbSNP | Ensembl ]. | VAR_038370 | |||||
| Natural variant | 43 | 1 | A → T. Corresponds to variant rs2066524 [ dbSNP | Ensembl ]. | VAR_021363 | |||||
| Natural variant | 114 | 1 | R → H. Corresponds to variant rs11555797 [ dbSNP | Ensembl ]. | VAR_021364 | |||||
| Natural variant | 206 | 1 | Y → D. Corresponds to variant rs5014982 [ dbSNP | Ensembl ]. | VAR_021365 | |||||
| Natural variant | 207 | 1 | I → F. Corresponds to variant rs6734114 [ dbSNP | Ensembl ]. | VAR_021366 | |||||
| Natural variant | 315 | 1 | S → R. Corresponds to variant rs2066522 [ dbSNP | Ensembl ]. | VAR_021367 | |||||
| Natural variant | 377 | 1 | E → Q. Ref.5 Ref.7 Corresponds to variant rs2066518 [ dbSNP | Ensembl ]. | VAR_021368 | |||||
| Natural variant | 424 | 1 | D → V. Corresponds to variant rs2066520 [ dbSNP | Ensembl ]. | VAR_021369 | |||||
| Natural variant | 432 | 1 | L → V in a breast cancer sample; somatic mutation. Ref.11 | VAR_036026 | |||||
| Natural variant | 468 | 1 | A → P in SIOD. Ref.2 | VAR_021370 | |||||
| Natural variant | 548 | 1 | I → N in SIOD. Ref.2 | VAR_021371 | |||||
| Natural variant | 579 | 1 | S → L in SIOD. Ref.2 | VAR_021372 | |||||
| Natural variant | 586 | 1 | R → W in SIOD; impairs without abolishing annealing helicase activity but still binds selectively to fork DNA relative to ssDNA or dsDNA. Ref.2 Ref.12 | VAR_021373 | |||||
| Natural variant | 644 | 1 | R → W in SIOD. Ref.2 | VAR_021374 | |||||
| Natural variant | 645 | 1 | R → C in SIOD. Ref.2 | VAR_021375 | |||||
| Natural variant | 647 | 1 | K → Q in SIOD. Ref.2 | VAR_021376 | |||||
| Natural variant | 647 | 1 | K → T in SIOD. Ref.2 | VAR_021377 | |||||
| Natural variant | 649 | 1 | D → N. Corresponds to variant rs2066523 [ dbSNP | Ensembl ]. | VAR_021378 | |||||
| Natural variant | 705 | 1 | T → I in SIOD. Ref.2 | VAR_021379 | |||||
| Natural variant | 742 | 1 | T → M. Corresponds to variant rs2271336 [ dbSNP | Ensembl ]. | VAR_021380 | |||||
| Natural variant | 764 | 1 | R → Q in SIOD; abolishes annealing helicase activity but still binds selectively to fork DNA relative to ssDNA or dsDNA. Ref.2 Ref.12 | VAR_021381 | |||||
| Natural variant | 820 | 1 | R → H in SIOD. Ref.2 | VAR_021382 | |||||
Experimental info | |||||||||
| Sequence conflict | 118 | 1 | A → T in AAF24984. Ref.1 | ||||||
| Sequence conflict | 335 | 1 | C → G in AAF24984. Ref.1 | ||||||
| Sequence conflict | 344 | 1 | E → K in BAA90955. Ref.7 | ||||||
| Sequence conflict | 882 | 1 | I → M in AAF24984. Ref.1 | ||||||
| Sequence conflict | 900 | 1 | L → V in AAF24984. Ref.1 | ||||||
| Sequence conflict | 911 | 1 | A → G in AAF24984. Ref.1 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse." Coleman M.A., Eisen J.A., Mohrenweiser H.W. Genomics 65:274-282(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY. |
| [2] | "Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia." Boerkoel C.F., Takashima H., John J., Yan J., Stankiewicz P., Rosenbarker L., Andre J.-L., Bogdanovic R., Burguet A., Cockfield S., Cordeiro I., Frund S., Illies F., Joseph M., Kaitila I., Lama G., Loirat C., McLeod D.R. Stockton D.W.Nat. Genet. 30:215-220(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, VARIANTS SIOD PRO-468; ASN-548; LEU-579; TRP-586; TRP-644; CYS-645; GLN-647; THR-647; ILE-705; GLN-764 AND HIS-820. |
| [3] | "Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. Wilson R.K.Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [5] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS GLY-22 AND GLN-377. Tissue: Lung and Lymph. |
| [6] | "The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 147-954. Tissue: Testis. |
| [7] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 335-954, VARIANT GLN-377. |
| [8] | "A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma. |
| [9] | "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-151, MASS SPECTROMETRY. Tissue: Cervix carcinoma. |
| [10] | "Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| [11] | "The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E.Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] VAL-432. |
| [12] | "HARP is an ATP-driven annealing helicase." Yusufzai T., Kadonaga J.T. Science 322:748-750(2008) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF VARIANTS SIOD TRP-586 AND GLN-764, FUNCTION, DNA-BINDING. |
| + | Additional computationally mapped references. |
Web resources
| SMARCAL1base SMARCAL1 mutation db |
| GeneReviews |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | AF082179 mRNA. Translation: AAF24984.1. AF210842 AF210841 Genomic DNA. Translation: AAF70454.1.AF432223 mRNA. Translation: AAL73034.1. AC098820 Genomic DNA. Translation: AAX93097.1. CH471063 Genomic DNA. Translation: EAW70567.1. BC016482 mRNA. Translation: AAH16482.1. BC043341 mRNA. Translation: AAH43341.1. AL122076 mRNA. Translation: CAB59251.1. AK000117 mRNA. Translation: BAA90955.1. Different initiation. |
| IPI | IPI00386311. |
| PIR | T34557. |
| RefSeq | NP_001120679.1. NM_001127207.1. NP_054859.2. NM_014140.3. |
| UniGene | Hs.516674. |
3D structure databases | |
| ProteinModelPortal | Q9NZC9. |
| ModBase | Search... |
Protein-protein interaction databases | |
| IntAct | Q9NZC9. 1 interaction. |
| MINT | MINT-8415341. |
| STRING | 9606.ENSP00000349823. |
PTM databases | |
| PhosphoSite | Q9NZC9. |
Polymorphism databases | |
| DMDM | 60390962. |
Proteomic databases | |
| PaxDb | Q9NZC9. |
| PRIDE | Q9NZC9. |
Protocols and materials databases | |
| DNASU | 50485. |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000357276; ENSP00000349823; ENSG00000138375. ENST00000358207; ENSP00000350940; ENSG00000138375. |
| GeneID | 50485. |
| KEGG | hsa:50485. |
| UCSC | uc002vgc.4. human. |
Organism-specific databases | |
| CTD | 50485. |
| GeneCards | GC02P217277. |
| HGNC | HGNC:11102. SMARCAL1. |
| HPA | HPA020337. |
| MIM | 242900. phenotype. 606622. gene. |
| neXtProt | NX_Q9NZC9. |
| Orphanet | 1830. Schimke immuno-osseous dysplasia. |
| PharmGKB | PA35952. |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | COG0553. |
| HOVERGEN | HBG054110. |
| InParanoid | Q9NZC9. |
| KO | K14440. |
| OMA | FKQQNLS. |
| OrthoDB | EOG4RFKRT. |
Gene expression databases | |
| ArrayExpress | Q9NZC9. |
| Bgee | Q9NZC9. |
| CleanEx | HS_SMARCAL1. |
| Genevestigator | Q9NZC9. |
| GermOnline | ENSG00000138375. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR010003. HARP_dom. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR027417. P-loop_NTPase. IPR000330. SNF2_N. [Graphical view] |
| Pfam | PF07443. HARP. 2 hits. PF00271. Helicase_C. 1 hit. PF00176. SNF2_N. 1 hit. [Graphical view] |
| SMART | SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view] |
| SUPFAM | SSF52540. SSF52540. 2 hits. |
| PROSITE | PS51467. HARP. 2 hits. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other | |
| GenomeRNAi | 50485. |
| NextBio | 53040. |
| SOURCE | Search... |
Entry information
| Entry name | SMAL1_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q9NZC9 Secondary accession number(s): A6NEH0 Q9UI93 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 2 Human chromosome 2: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with
